DE BAP1
Mafe Senosain
9/15/2020
Pre-processing of the data
ls_preprocessed <- preprocess_rna(path_rnaseq = 'rnaseq.RData', correct_batch = T, correct_gender = T)Exploring data
Batch effect correction
print(ls_preprocessed$pbatch_bf)
print(ls_preprocessed$pgender_bf)
print(ls_preprocessed$pbatch_af)
print(ls_preprocessed$pgender_af)
DE analysis
gn <- as.character(ls_preprocessed$rna_all$Feature[which(ls_preprocessed$rna_all$Feature_gene_name =='BAP1')])
DE_res <- DE_analysis(ls_preprocessed,
GeneBased=TRUE,
pDataBased=FALSE,
NewCondition=FALSE,
cond_nm= gn,
reference = 'low',
correct_gender=TRUE,
extremes_only=TRUE)## Unlist done## Labeling done## Filtering done## factor levels were dropped which had no samples## Design done## factor levels were dropped which had no samples## Warning: Setting row names on a tibble is deprecated.## vsd symbols done## using pre-existing size factors## estimating dispersions## gene-wise dispersion estimates## mean-dispersion relationship## final dispersion estimates## fitting model and testing## -- replacing outliers and refitting for 1192 genes
## -- DESeq argument 'minReplicatesForReplace' = 7
## -- original counts are preserved in counts(dds)## estimating dispersions## fitting model and testing## DESeq done## using 'normal' for LFC shrinkage, the Normal prior from Love et al (2014).
##
## Note that type='apeglm' and type='ashr' have shown to have less bias than type='normal'.
## See ?lfcShrink for more details on shrinkage type, and the DESeq2 vignette.
## Reference: https://doi.org/10.1093/bioinformatics/bty895## res symbols done## list doneDE results
heatmap_200(DE_res$res_df, DE_res$vsd_mat_sym, DE_res$meta_data, DE_res$pData_rnaseq)
x <- DE_res$res_df %>%
arrange(desc(abs(log2FoldChange)))
rownames(x) <- make.names(x$symbol, unique = T)
k <- gn
x <- x[-which(x$gene %in%k),]
#head(x, 10)
vp <- volcano_plot(x, gene=NULL, p_title='BAP1', pCutoff=0.001, FCcutoff=1.5)
List of genes differentially expressed (-1.5 > fold change > 1.5, pval<0.001)
vp_tb <- vp$data[which(vp$data$Sig == 'FC_P'),]
rownames(vp_tb) <- c(1:nrow(vp_tb))
kable(vp_tb)| baseMean | log2FoldChange | lfcSE | stat | pvalue | padj | gene | symbol | Sig | lab | xvals | yvals |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 6.395729e+01 | 3.905607 | 0.4079837 | 4.461556 | 0.0000081 | 0.0001766 | ENSG00000263076.1 | RPS9 | FC_P | RPS9 | 3.905607 | 0.0000081 |
| 7.434226e+01 | -3.602810 | 0.3643107 | -3.743773 | 0.0001813 | 0.0019834 | ENSG00000094755.12 | GABRP | FC_P | GABRP | -3.602810 | 0.0001813 |
| 3.568936e+02 | -3.477134 | 0.4061124 | -8.802162 | 0.0000000 | 0.0000000 | ENSG00000139144.5 | PIK3C2G | FC_P | PIK3C2G | -3.477134 | 0.0000000 |
| 1.364547e+02 | -3.181504 | 0.3879255 | -6.556765 | 0.0000000 | 0.0000000 | ENSG00000109511.6 | ANXA10 | FC_P | ANXA10 | -3.181504 | 0.0000000 |
| 5.915634e+00 | -3.075488 | 0.4096229 | -3.759272 | 0.0001704 | 0.0018910 | ENSG00000180251.4 | SLC9A4 | FC_P | SLC9A4 | -3.075488 | 0.0001704 |
| 1.680560e+02 | -2.851171 | 0.4087265 | -7.344544 | 0.0000000 | 0.0000000 | ENSG00000198758.6 | EPS8L3 | FC_P | EPS8L3 | -2.851171 | 0.0000000 |
| 3.089430e+01 | -2.779230 | 0.4053354 | -6.896032 | 0.0000000 | 0.0000000 | ENSG00000139151.10 | PLCZ1 | FC_P | PLCZ1 | -2.779230 | 0.0000000 |
| 8.698395e+00 | -2.763408 | 0.4376922 | -4.052550 | 0.0000507 | 0.0007386 | ENSG00000213759.4 | UGT2B11 | FC_P | UGT2B11 | -2.763408 | 0.0000507 |
| 1.700950e+01 | -2.663663 | 0.4038956 | -3.577265 | 0.0003472 | 0.0032632 | ENSG00000179674.2 | ARL14 | FC_P | ARL14 | -2.663663 | 0.0003472 |
| 1.565666e+01 | -2.659716 | 0.4341733 | -6.456752 | 0.0000000 | 0.0000000 | ENSG00000255960.1 | RP11-459D22.1 | FC_P | RP11.459D22.1 | -2.659716 | 0.0000000 |
| 8.598807e+00 | -2.537779 | 0.3983237 | -6.222362 | 0.0000000 | 0.0000001 | ENSG00000206918.1 | RNU6-1181P | FC_P | RNU6.1181P | -2.537779 | 0.0000000 |
| 1.703118e+01 | -2.437372 | 0.3881446 | -6.224429 | 0.0000000 | 0.0000001 | ENSG00000264727.1 | RP11-680C21.1 | FC_P | RP11.680C21.1 | -2.437372 | 0.0000000 |
| 5.309453e+01 | -2.432980 | 0.3995047 | -6.091562 | 0.0000000 | 0.0000001 | ENSG00000255745.1 | RP11-625L16.1 | FC_P | RP11.625L16.1 | -2.432980 | 0.0000000 |
| 4.953813e+01 | -2.421761 | 0.4028772 | -6.188719 | 0.0000000 | 0.0000001 | ENSG00000231738.6 | TSPAN19 | FC_P | TSPAN19 | -2.421761 | 0.0000000 |
| 5.463126e+01 | -2.361731 | 0.4178989 | -6.202472 | 0.0000000 | 0.0000001 | ENSG00000180861.5 | C12orf36 | FC_P | C12orf36 | -2.361731 | 0.0000000 |
| 1.050103e+01 | -2.256090 | 0.4354248 | -5.374849 | 0.0000001 | 0.0000042 | ENSG00000272609.1 | RP11-461M2.2 | FC_P | RP11.461M2.2 | -2.256090 | 0.0000001 |
| 1.777785e+03 | -2.246058 | 0.3260558 | -6.891107 | 0.0000000 | 0.0000000 | ENSG00000106258.9 | CYP3A5 | FC_P | CYP3A5 | -2.246058 | 0.0000000 |
| 1.145266e+01 | -2.221131 | 0.4247219 | -3.961601 | 0.0000744 | 0.0009940 | ENSG00000096006.7 | CRISP3 | FC_P | CRISP3 | -2.221131 | 0.0000744 |
| 3.845727e+02 | 2.216497 | 0.3960091 | 5.543714 | 0.0000000 | 0.0000020 | ENSG00000178343.4 | SHISA3 | FC_P | SHISA3 | 2.216497 | 0.0000000 |
| 4.740936e+01 | -2.211727 | 0.3842247 | -5.745174 | 0.0000000 | 0.0000008 | ENSG00000185860.9 | C1orf110 | FC_P | C1orf110 | -2.211727 | 0.0000000 |
| 2.762336e+00 | -2.189313 | 0.4089859 | -5.199607 | 0.0000002 | 0.0000092 | ENSG00000234497.1 | RP4-612J11.1 | FC_P | RP4.612J11.1 | -2.189313 | 0.0000002 |
| 9.540603e+00 | -2.167287 | 0.4045146 | -5.321060 | 0.0000001 | 0.0000054 | ENSG00000265374.1 | RP11-57J16.1 | FC_P | RP11.57J16.1 | -2.167287 | 0.0000001 |
| 6.927466e+00 | -2.161285 | 0.3843989 | -5.528617 | 0.0000000 | 0.0000021 | ENSG00000224493.1 | RP11-87O11.1 | FC_P | RP11.87O11.1 | -2.161285 | 0.0000000 |
| 2.699128e+00 | -2.150376 | 0.3770574 | -5.482018 | 0.0000000 | 0.0000026 | ENSG00000201392.1 | RNU6-1078P | FC_P | RNU6.1078P | -2.150376 | 0.0000000 |
| 2.632303e+00 | -2.136931 | 0.3878510 | -5.353384 | 0.0000001 | 0.0000047 | ENSG00000231080.1 | RP11-342H21.2 | FC_P | RP11.342H21.2 | -2.136931 | 0.0000001 |
| 1.046986e+02 | -2.136067 | 0.4013775 | -5.870197 | 0.0000000 | 0.0000004 | ENSG00000198643.2 | FAM3D | FC_P | FAM3D | -2.136067 | 0.0000000 |
| 8.313274e+01 | -2.126918 | 0.3681818 | -5.774856 | 0.0000000 | 0.0000007 | ENSG00000118492.12 | ADGB | FC_P | ADGB | -2.126918 | 0.0000000 |
| 6.619559e+00 | -2.122946 | 0.3769792 | -5.495207 | 0.0000000 | 0.0000024 | ENSG00000254878.1 | CTD-3096P4.1 | FC_P | CTD.3096P4.1 | -2.122946 | 0.0000000 |
| 2.223428e+02 | -2.121234 | 0.4131340 | -5.221776 | 0.0000002 | 0.0000084 | ENSG00000166959.3 | MS4A8 | FC_P | MS4A8 | -2.121234 | 0.0000002 |
| 9.753472e+00 | -2.119295 | 0.4378337 | -5.141038 | 0.0000003 | 0.0000118 | ENSG00000255892.1 | RP11-459D22.2 | FC_P | RP11.459D22.2 | -2.119295 | 0.0000003 |
| 3.292266e+00 | -2.117288 | 0.4184216 | -4.734363 | 0.0000022 | 0.0000632 | ENSG00000253622.1 | RP11-654G14.1 | FC_P | RP11.654G14.1 | -2.117288 | 0.0000022 |
| 3.057300e+01 | -2.102215 | 0.3593455 | -5.852412 | 0.0000000 | 0.0000004 | ENSG00000183644.9 | C11orf88 | FC_P | C11orf88 | -2.102215 | 0.0000000 |
| 3.057907e+00 | -2.099597 | 0.4040851 | -5.079014 | 0.0000004 | 0.0000154 | ENSG00000221436.1 | MIR548F3 | FC_P | MIR548F3 | -2.099597 | 0.0000004 |
| 1.887166e+01 | -2.092479 | 0.3489431 | -5.970496 | 0.0000000 | 0.0000003 | ENSG00000124564.13 | SLC17A3 | FC_P | SLC17A3 | -2.092479 | 0.0000000 |
| 3.284765e+01 | -2.069994 | 0.3722642 | -5.587361 | 0.0000000 | 0.0000016 | ENSG00000152936.6 | IFLTD1 | FC_P | IFLTD1 | -2.069994 | 0.0000000 |
| 5.937833e+00 | -2.062259 | 0.4092754 | -5.138920 | 0.0000003 | 0.0000119 | ENSG00000269916.1 | RP11-193M21.1 | FC_P | RP11.193M21.1 | -2.062259 | 0.0000003 |
| 1.454277e+02 | -2.043549 | 0.3876956 | -5.264933 | 0.0000001 | 0.0000069 | ENSG00000015520.10 | NPC1L1 | FC_P | NPC1L1 | -2.043549 | 0.0000001 |
| 3.642398e+02 | -2.040786 | 0.4052670 | -5.161997 | 0.0000002 | 0.0000108 | ENSG00000171747.4 | LGALS4 | FC_P | LGALS4 | -2.040786 | 0.0000002 |
| 4.116681e+00 | -2.023286 | 0.4150570 | -4.806811 | 0.0000015 | 0.0000468 | ENSG00000236164.1 | RP11-268F1.3 | FC_P | RP11.268F1.3 | -2.023286 | 0.0000015 |
| 3.250756e+01 | -2.018262 | 0.2342670 | -4.315903 | 0.0000159 | 0.0002980 | ENSG00000137860.7 | SLC28A2 | FC_P | SLC28A2 | -2.018262 | 0.0000159 |
| 1.147143e+01 | -2.015023 | 0.4319118 | -4.890826 | 0.0000010 | 0.0000333 | ENSG00000176571.7 | CNBD1 | FC_P | CNBD1 | -2.015023 | 0.0000010 |
| 3.843674e+02 | -2.008995 | 0.3289891 | -6.107607 | 0.0000000 | 0.0000001 | ENSG00000174844.10 | DNAH12 | FC_P | DNAH12 | -2.008995 | 0.0000000 |
| 5.518288e+01 | -1.994169 | 0.3984189 | -4.943332 | 0.0000008 | 0.0000269 | ENSG00000113303.7 | BTNL8 | FC_P | BTNL8 | -1.994169 | 0.0000008 |
| 3.534691e+01 | -1.972888 | 0.4013390 | -4.933334 | 0.0000008 | 0.0000281 | ENSG00000224259.1 | RP11-48O20.4 | FC_P | RP11.48O20.4 | -1.972888 | 0.0000008 |
| 1.913498e+02 | -1.972476 | 0.3265393 | -6.078994 | 0.0000000 | 0.0000001 | ENSG00000179813.2 | FAM216B | FC_P | FAM216B | -1.972476 | 0.0000000 |
| 2.915134e+00 | -1.967581 | 0.4173450 | -4.620100 | 0.0000038 | 0.0000986 | ENSG00000250961.1 | CTD-2023N9.1 | FC_P | CTD.2023N9.1 | -1.967581 | 0.0000038 |
| 6.459530e+00 | -1.955358 | 0.4266388 | -4.812671 | 0.0000015 | 0.0000456 | ENSG00000109205.12 | ODAM | FC_P | ODAM | -1.955358 | 0.0000015 |
| 1.060466e+02 | -1.950554 | 0.4303060 | -4.570237 | 0.0000049 | 0.0001187 | ENSG00000101076.12 | HNF4A | FC_P | HNF4A | -1.950554 | 0.0000049 |
| 4.903937e+01 | -1.941008 | 0.3795627 | -4.909471 | 0.0000009 | 0.0000310 | ENSG00000259871.1 | CTA-363E6.1 | FC_P | CTA.363E6.1 | -1.941008 | 0.0000009 |
| 1.654734e+01 | -1.927166 | 0.3398336 | -5.655685 | 0.0000000 | 0.0000012 | ENSG00000152595.12 | MEPE | FC_P | MEPE | -1.927166 | 0.0000000 |
| 4.787161e+01 | 1.922242 | 0.3860571 | 5.020664 | 0.0000005 | 0.0000194 | ENSG00000156959.7 | LHFPL4 | FC_P | LHFPL4 | 1.922242 | 0.0000005 |
| 1.619878e+01 | -1.914762 | 0.3512283 | -5.458547 | 0.0000000 | 0.0000029 | ENSG00000178125.10 | PPP1R42 | FC_P | PPP1R42 | -1.914762 | 0.0000000 |
| 1.402639e+01 | -1.914343 | 0.3519080 | -5.434830 | 0.0000001 | 0.0000032 | ENSG00000111404.2 | RERGL | FC_P | RERGL | -1.914343 | 0.0000001 |
| 4.324700e+00 | -1.908944 | 0.4002577 | -4.751821 | 0.0000020 | 0.0000588 | ENSG00000259833.1 | RP11-23E19.1 | FC_P | RP11.23E19.1 | -1.908944 | 0.0000020 |
| 1.723749e+03 | -1.908686 | 0.4054201 | -4.736682 | 0.0000022 | 0.0000625 | ENSG00000125999.6 | BPIFB1 | FC_P | BPIFB1 | -1.908686 | 0.0000022 |
| 1.394267e+01 | -1.901706 | 0.4356505 | -4.593225 | 0.0000044 | 0.0001090 | ENSG00000257454.1 | CTD-2021H9.2 | FC_P | CTD.2021H9.2 | -1.901706 | 0.0000044 |
| 1.399229e+01 | -1.898384 | 0.3520687 | -5.372038 | 0.0000001 | 0.0000043 | ENSG00000231204.1 | AC011752.1 | FC_P | AC011752.1 | -1.898384 | 0.0000001 |
| 6.104181e+00 | -1.896846 | 0.3201263 | -5.924827 | 0.0000000 | 0.0000003 | ENSG00000265042.1 | AL137800.1 | FC_P | AL137800.1 | -1.896846 | 0.0000000 |
| 6.337819e+00 | -1.885726 | 0.4142377 | -4.584775 | 0.0000045 | 0.0001125 | ENSG00000230739.1 | RP11-331H2.4 | FC_P | RP11.331H2.4 | -1.885726 | 0.0000045 |
| 5.324843e+01 | -1.874704 | 0.3643601 | -5.180296 | 0.0000002 | 0.0000100 | ENSG00000231980.1 | AC011899.10 | FC_P | AC011899.10 | -1.874704 | 0.0000002 |
| 1.711681e+02 | -1.864090 | 0.3677366 | -5.088596 | 0.0000004 | 0.0000147 | ENSG00000169064.8 | ZBBX | FC_P | ZBBX | -1.864090 | 0.0000004 |
| 4.820517e+01 | -1.863829 | 0.4361304 | -4.991890 | 0.0000006 | 0.0000221 | ENSG00000205922.4 | ONECUT3 | FC_P | ONECUT3 | -1.863829 | 0.0000006 |
| 1.055252e+03 | -1.862965 | 0.3902522 | -4.904527 | 0.0000009 | 0.0000315 | ENSG00000127324.4 | TSPAN8 | FC_P | TSPAN8 | -1.862965 | 0.0000009 |
| 1.017633e+01 | -1.853212 | 0.3935168 | -4.807918 | 0.0000015 | 0.0000467 | ENSG00000236460.1 | SNX2P2 | FC_P | SNX2P2 | -1.853212 | 0.0000015 |
| 1.260226e+02 | -1.845505 | 0.3475012 | -5.323896 | 0.0000001 | 0.0000053 | ENSG00000170324.15 | FRMPD2 | FC_P | FRMPD2 | -1.845505 | 0.0000001 |
| 1.157815e+01 | -1.834585 | 0.4364329 | -4.584523 | 0.0000046 | 0.0001126 | ENSG00000229005.2 | RP5-881L22.4 | FC_P | RP5.881L22.4 | -1.834585 | 0.0000046 |
| 2.377084e+02 | -1.828788 | 0.3705012 | -4.817670 | 0.0000015 | 0.0000446 | ENSG00000254608.1 | RP11-56A10.1 | FC_P | RP11.56A10.1 | -1.828788 | 0.0000015 |
| 4.557000e+00 | -1.826705 | 0.4054238 | -4.466473 | 0.0000080 | 0.0001739 | ENSG00000232462.1 | RP11-13E1.5 | FC_P | RP11.13E1.5 | -1.826705 | 0.0000080 |
| 2.690914e+01 | -1.822595 | 0.4110993 | -4.486034 | 0.0000073 | 0.0001611 | ENSG00000186329.5 | TMEM212 | FC_P | TMEM212 | -1.822595 | 0.0000073 |
| 1.006642e+01 | 1.815546 | 0.4017259 | 4.335830 | 0.0000145 | 0.0002796 | ENSG00000227656.3 | RPL3P2 | FC_P | RPL3P2 | 1.815546 | 0.0000145 |
| 1.067424e+02 | -1.808680 | 0.3697544 | -5.089734 | 0.0000004 | 0.0000147 | ENSG00000115616.2 | SLC9A2 | FC_P | SLC9A2 | -1.808680 | 0.0000004 |
| 2.800994e+01 | -1.805767 | 0.3778649 | -4.796064 | 0.0000016 | 0.0000489 | ENSG00000152611.7 | CAPSL | FC_P | CAPSL | -1.805767 | 0.0000016 |
| 7.954587e+01 | -1.804249 | 0.4028713 | -4.263718 | 0.0000201 | 0.0003557 | ENSG00000144852.12 | NR1I2 | FC_P | NR1I2 | -1.804249 | 0.0000201 |
| 3.353307e+01 | -1.803266 | 0.3597823 | -5.000164 | 0.0000006 | 0.0000212 | ENSG00000231606.1 | RP11-344F13.1 | FC_P | RP11.344F13.1 | -1.803266 | 0.0000006 |
| 6.697073e+00 | -1.803135 | 0.4347802 | -4.650053 | 0.0000033 | 0.0000883 | ENSG00000170788.9 | DYDC1 | FC_P | DYDC1 | -1.803135 | 0.0000033 |
| 3.387660e+02 | -1.794276 | 0.4286749 | -4.220637 | 0.0000244 | 0.0004161 | ENSG00000183778.13 | B3GALT5 | FC_P | B3GALT5 | -1.794276 | 0.0000244 |
| 3.627475e+01 | -1.792554 | 0.3756921 | -4.752823 | 0.0000020 | 0.0000586 | ENSG00000197826.7 | C4orf22 | FC_P | C4orf22 | -1.792554 | 0.0000020 |
| 2.899941e+01 | -1.788535 | 0.4356225 | -4.513469 | 0.0000064 | 0.0001457 | ENSG00000233377.1 | MTND4P20 | FC_P | MTND4P20 | -1.788535 | 0.0000064 |
| 4.812892e+00 | -1.787645 | 0.3699238 | -4.844228 | 0.0000013 | 0.0000402 | ENSG00000272508.1 | RP11-96C23.14 | FC_P | RP11.96C23.14 | -1.787645 | 0.0000013 |
| 2.953442e+01 | -1.787242 | 0.4050641 | -4.748168 | 0.0000021 | 0.0000596 | ENSG00000153822.9 | KCNJ16 | FC_P | KCNJ16 | -1.787242 | 0.0000021 |
| 2.071817e+02 | -1.786619 | 0.3557032 | -5.359911 | 0.0000001 | 0.0000046 | ENSG00000173597.4 | SULT1B1 | FC_P | SULT1B1 | -1.786619 | 0.0000001 |
| 1.214391e+01 | -1.777301 | 0.2873209 | -6.154611 | 0.0000000 | 0.0000001 | ENSG00000212259.1 | RNU6-308P | FC_P | RNU6.308P | -1.777301 | 0.0000000 |
| 2.772308e+00 | -1.765928 | 0.4335961 | -4.246971 | 0.0000217 | 0.0003783 | ENSG00000199798.1 | SNORD114-5 | FC_P | SNORD114.5 | -1.765928 | 0.0000217 |
| 1.376221e+01 | -1.760880 | 0.3927977 | -4.968263 | 0.0000007 | 0.0000242 | ENSG00000212384.1 | SNORD113-2 | FC_P | SNORD113.2 | -1.760880 | 0.0000007 |
| 1.186392e+03 | 1.758429 | 0.3258986 | 5.672778 | 0.0000000 | 0.0000011 | ENSG00000272060.1 | RNA18S5 | FC_P | RNA18S5 | 1.758429 | 0.0000000 |
| 7.782392e+00 | -1.742614 | 0.3480489 | -4.976612 | 0.0000006 | 0.0000233 | ENSG00000252145.1 | RNU6-1225P | FC_P | RNU6.1225P | -1.742614 | 0.0000006 |
| 5.614511e+00 | -1.741985 | 0.3239441 | -5.322892 | 0.0000001 | 0.0000053 | ENSG00000267316.1 | RP11-879F14.3 | FC_P | RP11.879F14.3 | -1.741985 | 0.0000001 |
| 5.588912e+01 | -1.736783 | 0.3761547 | -4.626557 | 0.0000037 | 0.0000961 | ENSG00000176034.8 | CHDC2 | FC_P | CHDC2 | -1.736783 | 0.0000037 |
| 3.671876e+01 | -1.735247 | 0.3888346 | -4.132938 | 0.0000358 | 0.0005608 | ENSG00000179008.4 | C14orf39 | FC_P | C14orf39 | -1.735247 | 0.0000358 |
| 2.799997e+01 | -1.733726 | 0.4264337 | -4.232982 | 0.0000231 | 0.0003975 | ENSG00000258053.1 | CTD-2021H9.3 | FC_P | CTD.2021H9.3 | -1.733726 | 0.0000231 |
| 2.476614e+01 | -1.732557 | 0.3719044 | -4.806639 | 0.0000015 | 0.0000468 | ENSG00000116785.9 | CFHR3 | FC_P | CFHR3 | -1.732557 | 0.0000015 |
| 6.709973e+00 | -1.730895 | 0.3949433 | -4.469892 | 0.0000078 | 0.0001717 | ENSG00000231688.1 | RPL21P43 | FC_P | RPL21P43 | -1.730895 | 0.0000078 |
| 4.280093e+00 | -1.725939 | 0.4206881 | -4.133070 | 0.0000358 | 0.0005607 | ENSG00000272474.1 | SNORD113-5 | FC_P | SNORD113.5 | -1.725939 | 0.0000358 |
| 2.252063e+02 | 1.725812 | 0.4345496 | 3.674346 | 0.0002385 | 0.0024535 | ENSG00000184937.8 | WT1 | FC_P | WT1 | 1.725812 | 0.0002385 |
| 8.437506e+01 | -1.725060 | 0.3861698 | -4.336275 | 0.0000145 | 0.0002793 | ENSG00000261210.1 | CLEC19A | FC_P | CLEC19A | -1.725060 | 0.0000145 |
| 2.357202e+01 | -1.722434 | 0.3038579 | -5.690980 | 0.0000000 | 0.0000010 | ENSG00000201852.1 | RNU6-702P | FC_P | RNU6.702P | -1.722434 | 0.0000000 |
| 9.747567e+01 | -1.721685 | 0.3738661 | -4.475010 | 0.0000076 | 0.0001686 | ENSG00000188477.8 | AC003003.5 | FC_P | AC003003.5 | -1.721685 | 0.0000076 |
| 6.351681e+00 | -1.720670 | 0.4069225 | -4.285843 | 0.0000182 | 0.0003318 | ENSG00000213579.3 | RP4-595K12.1 | FC_P | RP4.595K12.1 | -1.720670 | 0.0000182 |
| 9.808668e+00 | 1.718650 | 0.3632088 | 4.523860 | 0.0000061 | 0.0001405 | ENSG00000238531.1 | SNORD105B | FC_P | SNORD105B | 1.718650 | 0.0000061 |
| 2.341197e+00 | -1.715618 | 0.4330651 | -3.833136 | 0.0001265 | 0.0014934 | ENSG00000252266.1 | Y_RNA | FC_P | Y_RNA | -1.715618 | 0.0001265 |
| 4.709991e+00 | -1.711718 | 0.3470465 | -4.896369 | 0.0000010 | 0.0000327 | ENSG00000207769.1 | MIR586 | FC_P | MIR586 | -1.711718 | 0.0000010 |
| 8.961454e+00 | -1.705116 | 0.2895962 | -5.930252 | 0.0000000 | 0.0000003 | ENSG00000199551.1 | RNU6-545P | FC_P | RNU6.545P | -1.705116 | 0.0000000 |
| 6.418227e+00 | -1.705062 | 0.4094651 | -4.149423 | 0.0000333 | 0.0005303 | ENSG00000225738.2 | NRG3-AS1 | FC_P | NRG3.AS1 | -1.705062 | 0.0000333 |
| 4.311073e+00 | -1.702169 | 0.4272429 | -3.993381 | 0.0000651 | 0.0008962 | ENSG00000253500.1 | AF121898.3 | FC_P | AF121898.3 | -1.702169 | 0.0000651 |
| 1.395055e+02 | -1.698388 | 0.3846098 | -4.431054 | 0.0000094 | 0.0001989 | ENSG00000178965.9 | C1orf173 | FC_P | C1orf173 | -1.698388 | 0.0000094 |
| 1.857221e+02 | -1.697836 | 0.4355724 | -3.737769 | 0.0001857 | 0.0020190 | ENSG00000006611.11 | USH1C | FC_P | USH1C | -1.697836 | 0.0001857 |
| 2.710706e+01 | -1.695581 | 0.3826837 | -4.350390 | 0.0000136 | 0.0002666 | ENSG00000253496.2 | RP11-13N12.1 | FC_P | RP11.13N12.1 | -1.695581 | 0.0000136 |
| 2.727041e+01 | 1.694221 | 0.4377222 | 4.317120 | 0.0000158 | 0.0002968 | ENSG00000229544.6 | NKX1-2 | FC_P | NKX1.2 | 1.694221 | 0.0000158 |
| 8.485052e+02 | 1.687851 | 0.2883636 | 5.803415 | 0.0000000 | 0.0000006 | ENSG00000266219.1 | AL592188.8 | FC_P | AL592188.8 | 1.687851 | 0.0000000 |
| 1.470123e+02 | 1.687124 | 0.3085721 | 5.392887 | 0.0000001 | 0.0000039 | ENSG00000252139.1 | SCARNA18 | FC_P | SCARNA18 | 1.687124 | 0.0000001 |
| 9.626820e+00 | -1.686557 | 0.3331058 | -5.200573 | 0.0000002 | 0.0000091 | ENSG00000253576.1 | GS1-5L10.1 | FC_P | GS1.5L10.1 | -1.686557 | 0.0000002 |
| 2.313546e+01 | -1.685894 | 0.2733041 | -6.253703 | 0.0000000 | 0.0000001 | ENSG00000258026.1 | RP11-543H12.1 | FC_P | RP11.543H12.1 | -1.685894 | 0.0000000 |
| 6.219826e+00 | -1.683636 | 0.4240010 | -3.965518 | 0.0000732 | 0.0009812 | ENSG00000255993.1 | PSMC1P9 | FC_P | PSMC1P9 | -1.683636 | 0.0000732 |
| 1.988843e+01 | -1.678026 | 0.2695354 | -6.221283 | 0.0000000 | 0.0000001 | ENSG00000234523.1 | NDUFB1P2 | FC_P | NDUFB1P2 | -1.678026 | 0.0000000 |
| 5.995542e+01 | -1.672144 | 0.3507616 | -4.784304 | 0.0000017 | 0.0000514 | ENSG00000170703.11 | TTLL6 | FC_P | TTLL6 | -1.672144 | 0.0000017 |
| 2.595302e+01 | -1.670899 | 0.3929936 | -4.280856 | 0.0000186 | 0.0003374 | ENSG00000133115.7 | STOML3 | FC_P | STOML3 | -1.670899 | 0.0000186 |
| 9.164636e+00 | -1.667301 | 0.2625477 | -6.319647 | 0.0000000 | 0.0000000 | ENSG00000216205.1 | AC036178.1 | FC_P | AC036178.1 | -1.667301 | 0.0000000 |
| 2.574318e+01 | -1.663684 | 0.3530013 | -3.392622 | 0.0006923 | 0.0055673 | ENSG00000122012.9 | SV2C | FC_P | SV2C | -1.663684 | 0.0006923 |
| 9.447488e+02 | -1.658676 | 0.3765336 | -4.116985 | 0.0000384 | 0.0005914 | ENSG00000104237.6 | RP1 | FC_P | RP1 | -1.658676 | 0.0000384 |
| 7.777534e+00 | -1.657092 | 0.3628047 | -4.537816 | 0.0000057 | 0.0001341 | ENSG00000223015.1 | RNU6-1135P | FC_P | RNU6.1135P | -1.657092 | 0.0000057 |
| 1.077423e+02 | -1.657082 | 0.2425042 | -6.846682 | 0.0000000 | 0.0000000 | ENSG00000117501.10 | MROH9 | FC_P | MROH9 | -1.657082 | 0.0000000 |
| 2.692793e+01 | 1.655353 | 0.3899967 | 3.785196 | 0.0001536 | 0.0017410 | ENSG00000210077.1 | MT-TV | FC_P | MT.TV | 1.655353 | 0.0001536 |
| 4.702193e+00 | 1.653824 | 0.4018464 | 4.138235 | 0.0000350 | 0.0005508 | ENSG00000229172.1 | AC073065.3 | FC_P | AC073065.3 | 1.653824 | 0.0000350 |
| 5.030414e+00 | -1.652382 | 0.3793573 | -4.481994 | 0.0000074 | 0.0001638 | ENSG00000221249.1 | AC004980.1 | FC_P | AC004980.1 | -1.652382 | 0.0000074 |
| 2.152592e+01 | -1.651480 | 0.3030535 | -5.625535 | 0.0000000 | 0.0000013 | ENSG00000271730.1 | RP11-787I22.3 | FC_P | RP11.787I22.3 | -1.651480 | 0.0000000 |
| 2.921686e+01 | 1.649626 | 0.3594210 | 4.578599 | 0.0000047 | 0.0001151 | ENSG00000115138.6 | POMC | FC_P | POMC | 1.649626 | 0.0000047 |
| 6.892794e+00 | -1.647152 | 0.4081034 | -4.084261 | 0.0000442 | 0.0006606 | ENSG00000256717.1 | AP000797.3 | FC_P | AP000797.3 | -1.647152 | 0.0000442 |
| 1.502092e+00 | -1.646279 | 0.4321745 | -3.669846 | 0.0002427 | 0.0024882 | ENSG00000238770.1 | snoU13 | FC_P | snoU13 | -1.646279 | 0.0002427 |
| 6.298731e+00 | -1.644446 | 0.3574308 | -4.531219 | 0.0000059 | 0.0001366 | ENSG00000264470.1 | MIR4794 | FC_P | MIR4794 | -1.644446 | 0.0000059 |
| 7.878457e+01 | -1.643886 | 0.3513834 | -4.947666 | 0.0000008 | 0.0000264 | ENSG00000200389.1 | RNU6-509P | FC_P | RNU6.509P | -1.643886 | 0.0000008 |
| 5.188219e+00 | -1.639926 | 0.4230211 | -4.085930 | 0.0000439 | 0.0006566 | ENSG00000240666.1 | MME-AS1 | FC_P | MME.AS1 | -1.639926 | 0.0000439 |
| 8.337960e+01 | -1.638588 | 0.3654787 | -4.487690 | 0.0000072 | 0.0001602 | ENSG00000165164.8 | CXorf22 | FC_P | CXorf22 | -1.638588 | 0.0000072 |
| 1.383801e+01 | 1.633614 | 0.4025336 | 3.744339 | 0.0001809 | 0.0019801 | ENSG00000237222.3 | AC090505.6 | FC_P | AC090505.6 | 1.633614 | 0.0001809 |
| 8.191233e+01 | -1.632666 | 0.3806674 | -4.093422 | 0.0000425 | 0.0006403 | ENSG00000223561.2 | AC003090.1 | FC_P | AC003090.1 | -1.632666 | 0.0000425 |
| 9.166382e+00 | -1.630897 | 0.3795985 | -4.275920 | 0.0000190 | 0.0003429 | ENSG00000080572.8 | PIH1D3 | FC_P | PIH1D3 | -1.630897 | 0.0000190 |
| 2.196298e+01 | -1.627392 | 0.3102061 | -5.252599 | 0.0000001 | 0.0000073 | ENSG00000257467.1 | RP11-121G22.3 | FC_P | RP11.121G22.3 | -1.627392 | 0.0000001 |
| 5.341559e+00 | -1.625179 | 0.3598192 | -4.437266 | 0.0000091 | 0.0001938 | ENSG00000246016.2 | RP11-1C1.7 | FC_P | RP11.1C1.7 | -1.625179 | 0.0000091 |
| 1.228739e+01 | -1.624600 | 0.3252000 | -5.023798 | 0.0000005 | 0.0000192 | ENSG00000239119.1 | RNU7-119P | FC_P | RNU7.119P | -1.624600 | 0.0000005 |
| 1.342024e+01 | -1.622414 | 0.2778539 | -5.868876 | 0.0000000 | 0.0000004 | ENSG00000206700.1 | RNU6-723P | FC_P | RNU6.723P | -1.622414 | 0.0000000 |
| 9.077770e+00 | -1.618259 | 0.2876106 | -5.678807 | 0.0000000 | 0.0000011 | ENSG00000199790.1 | RNU6-836P | FC_P | RNU6.836P | -1.618259 | 0.0000000 |
| 9.915807e+00 | -1.617854 | 0.4114030 | -4.034653 | 0.0000547 | 0.0007835 | ENSG00000255666.1 | RP11-867G2.6 | FC_P | RP11.867G2.6 | -1.617854 | 0.0000547 |
| 1.198596e+01 | -1.617547 | 0.3742146 | -4.341998 | 0.0000141 | 0.0002737 | ENSG00000227274.1 | AC005358.3 | FC_P | AC005358.3 | -1.617547 | 0.0000141 |
| 3.609974e+00 | -1.616071 | 0.3590620 | -4.570040 | 0.0000049 | 0.0001187 | ENSG00000201984.1 | Y_RNA | FC_P | Y_RNA.1 | -1.616071 | 0.0000049 |
| 1.228715e+01 | 1.614902 | 0.3584603 | 4.449898 | 0.0000086 | 0.0001845 | ENSG00000146090.11 | RASGEF1C | FC_P | RASGEF1C | 1.614902 | 0.0000086 |
| 3.500915e+01 | -1.613115 | 0.3701629 | -4.358204 | 0.0000131 | 0.0002582 | ENSG00000148584.10 | A1CF | FC_P | A1CF | -1.613115 | 0.0000131 |
| 1.194109e+05 | 1.612413 | 0.2696172 | 5.942833 | 0.0000000 | 0.0000003 | ENSG00000264462.1 | MIR3648 | FC_P | MIR3648 | 1.612413 | 0.0000000 |
| 9.589887e+00 | -1.610169 | 0.4021951 | -4.015403 | 0.0000593 | 0.0008330 | ENSG00000188729.2 | OSTN | FC_P | OSTN | -1.610169 | 0.0000593 |
| 1.338768e+00 | -1.609817 | 0.4331838 | -3.738311 | 0.0001853 | 0.0020170 | ENSG00000235858.1 | RP11-36D19.8 | FC_P | RP11.36D19.8 | -1.609817 | 0.0001853 |
| 1.176743e+03 | 1.607707 | 0.2946436 | 5.461828 | 0.0000000 | 0.0000029 | ENSG00000160200.13 | CBS | FC_P | CBS | 1.607707 | 0.0000000 |
| 2.057098e+01 | -1.606989 | 0.3661343 | -4.298652 | 0.0000172 | 0.0003159 | ENSG00000100012.7 | SEC14L3 | FC_P | SEC14L3 | -1.606989 | 0.0000172 |
| 7.418793e+01 | -1.606235 | 0.3631896 | -4.555501 | 0.0000052 | 0.0001256 | ENSG00000153233.8 | PTPRR | FC_P | PTPRR | -1.606235 | 0.0000052 |
| 4.971652e+01 | -1.604928 | 0.3807218 | -4.235823 | 0.0000228 | 0.0003938 | ENSG00000124237.5 | C20orf85 | FC_P | C20orf85 | -1.604928 | 0.0000228 |
| 1.953535e+00 | -1.603849 | 0.4243566 | -3.702951 | 0.0002131 | 0.0022508 | ENSG00000260951.1 | RP5-978I12.1 | FC_P | RP5.978I12.1 | -1.603849 | 0.0002131 |
| 5.609159e+01 | -1.601879 | 0.3614049 | -4.530778 | 0.0000059 | 0.0001368 | ENSG00000162078.7 | ZG16B | FC_P | ZG16B | -1.601879 | 0.0000059 |
| 7.926429e+00 | -1.599889 | 0.4159279 | -3.897939 | 0.0000970 | 0.0012156 | ENSG00000012504.9 | NR1H4 | FC_P | NR1H4 | -1.599889 | 0.0000970 |
| 1.287067e+02 | -1.595846 | 0.4306239 | -4.025676 | 0.0000568 | 0.0008053 | ENSG00000166670.5 | MMP10 | FC_P | MMP10 | -1.595846 | 0.0000568 |
| 3.109340e+00 | -1.594509 | 0.4348478 | -4.104739 | 0.0000405 | 0.0006167 | ENSG00000268566.1 | RP11-687D19.1 | FC_P | RP11.687D19.1 | -1.594509 | 0.0000405 |
| 4.556154e+00 | -1.593594 | 0.4252739 | -4.007675 | 0.0000613 | 0.0008547 | ENSG00000200406.1 | SNORD114-23 | FC_P | SNORD114.23 | -1.593594 | 0.0000613 |
| 2.058356e+00 | -1.585759 | 0.4259552 | -3.720967 | 0.0001985 | 0.0021322 | ENSG00000261480.1 | RP11-578F21.6 | FC_P | RP11.578F21.6 | -1.585759 | 0.0001985 |
| 2.436957e+01 | -1.585755 | 0.3414095 | -4.643281 | 0.0000034 | 0.0000905 | ENSG00000255555.1 | AP000857.3 | FC_P | AP000857.3 | -1.585755 | 0.0000034 |
| 1.769750e+01 | -1.584630 | 0.3374153 | -4.718208 | 0.0000024 | 0.0000676 | ENSG00000259590.1 | RP11-20G13.3 | FC_P | RP11.20G13.3 | -1.584630 | 0.0000024 |
| 3.037435e+00 | -1.583881 | 0.4358179 | -3.799113 | 0.0001452 | 0.0016698 | ENSG00000118271.5 | TTR | FC_P | TTR | -1.583881 | 0.0001452 |
| 8.163824e+01 | -1.583481 | 0.3471961 | -4.632491 | 0.0000036 | 0.0000940 | ENSG00000114204.10 | SERPINI2 | FC_P | SERPINI2 | -1.583481 | 0.0000036 |
| 2.325209e+03 | 1.583043 | 0.3464355 | 4.460830 | 0.0000082 | 0.0001769 | ENSG00000200795.1 | RNU4-1 | FC_P | RNU4.1 | 1.583043 | 0.0000082 |
| 1.152383e+02 | -1.582556 | 0.3782377 | -4.007530 | 0.0000614 | 0.0008549 | ENSG00000254142.2 | RP11-53M11.3 | FC_P | RP11.53M11.3 | -1.582556 | 0.0000614 |
| 1.221791e+02 | -1.580080 | 0.3069198 | -5.194759 | 0.0000002 | 0.0000094 | ENSG00000100557.5 | C14orf105 | FC_P | C14orf105 | -1.580080 | 0.0000002 |
| 4.224641e+02 | -1.579226 | 0.3767903 | -4.284184 | 0.0000183 | 0.0003338 | ENSG00000137968.12 | SLC44A5 | FC_P | SLC44A5 | -1.579226 | 0.0000183 |
| 5.322447e+00 | 1.578842 | 0.2954826 | 5.289073 | 0.0000001 | 0.0000062 | ENSG00000237264.4 | FTH1P11 | FC_P | FTH1P11 | 1.578842 | 0.0000001 |
| 6.950779e+01 | -1.578497 | 0.2519516 | -6.424197 | 0.0000000 | 0.0000000 | ENSG00000262529.1 | CTA-276F8.2 | FC_P | CTA.276F8.2 | -1.578497 | 0.0000000 |
| 1.245443e+01 | 1.577743 | 0.3912442 | 4.002924 | 0.0000626 | 0.0008688 | ENSG00000199990.1 | VTRNA1-1 | FC_P | VTRNA1.1 | 1.577743 | 0.0000626 |
| 1.174347e+01 | -1.576298 | 0.3774081 | -4.147725 | 0.0000336 | 0.0005336 | ENSG00000242268.2 | RP11-368I23.2 | FC_P | RP11.368I23.2 | -1.576298 | 0.0000336 |
| 4.319028e+00 | -1.574790 | 0.3953339 | -3.960813 | 0.0000747 | 0.0009963 | ENSG00000226409.1 | RP11-735G4.1 | FC_P | RP11.735G4.1 | -1.574790 | 0.0000747 |
| 5.758443e+00 | -1.572808 | 0.4042124 | -3.741475 | 0.0001829 | 0.0019958 | ENSG00000250458.2 | RP11-107E21.1 | FC_P | RP11.107E21.1 | -1.572808 | 0.0001829 |
| 4.351673e+01 | 1.571434 | 0.3941555 | 3.622933 | 0.0002913 | 0.0028535 | ENSG00000105697.3 | HAMP | FC_P | HAMP | 1.571434 | 0.0002913 |
| 5.105132e+02 | -1.570643 | 0.3691072 | -4.271152 | 0.0000194 | 0.0003471 | ENSG00000007174.13 | DNAH9 | FC_P | DNAH9 | -1.570643 | 0.0000194 |
| 4.743095e+02 | -1.570048 | 0.3117129 | -5.101661 | 0.0000003 | 0.0000139 | ENSG00000154678.12 | PDE1C | FC_P | PDE1C | -1.570048 | 0.0000003 |
| 1.801050e+01 | 1.567729 | 0.3692785 | 4.004470 | 0.0000622 | 0.0008638 | ENSG00000216866.4 | RPS2P55 | FC_P | RPS2P55 | 1.567729 | 0.0000622 |
| 4.369468e+00 | -1.566920 | 0.3462177 | -4.455278 | 0.0000084 | 0.0001810 | ENSG00000232524.1 | RP11-332K15.1 | FC_P | RP11.332K15.1 | -1.566920 | 0.0000084 |
| 1.880953e+01 | -1.564362 | 0.4153869 | -3.829827 | 0.0001282 | 0.0015080 | ENSG00000157330.5 | C1orf158 | FC_P | C1orf158 | -1.564362 | 0.0001282 |
| 3.260924e+00 | -1.564137 | 0.4185901 | -3.665228 | 0.0002471 | 0.0025225 | ENSG00000225437.1 | RP1-257A15.1 | FC_P | RP1.257A15.1 | -1.564137 | 0.0002471 |
| 5.889510e+00 | -1.563054 | 0.3876942 | -4.328127 | 0.0000150 | 0.0002866 | ENSG00000234953.2 | RP5-837I24.2 | FC_P | RP5.837I24.2 | -1.563054 | 0.0000150 |
| 8.225308e+00 | -1.562651 | 0.4247699 | -3.673057 | 0.0002397 | 0.0024625 | ENSG00000218476.2 | RP11-108N13.1 | FC_P | RP11.108N13.1 | -1.562651 | 0.0002397 |
| 1.671937e+01 | -1.561706 | 0.2657241 | -5.937160 | 0.0000000 | 0.0000003 | ENSG00000238386.1 | RNU7-48P | FC_P | RNU7.48P | -1.561706 | 0.0000000 |
| 1.212337e+01 | -1.561638 | 0.3452121 | -4.532821 | 0.0000058 | 0.0001361 | ENSG00000216022.1 | AC068062.1 | FC_P | AC068062.1 | -1.561638 | 0.0000058 |
| 1.888402e+04 | 1.560446 | 0.2773541 | 5.573725 | 0.0000000 | 0.0000017 | ENSG00000169710.6 | FASN | FC_P | FASN | 1.560446 | 0.0000000 |
| 1.365552e+01 | -1.560404 | 0.3898377 | -3.990055 | 0.0000661 | 0.0009061 | ENSG00000244649.2 | CTD-2377D24.6 | FC_P | CTD.2377D24.6 | -1.560404 | 0.0000661 |
| 8.004087e+01 | -1.559638 | 0.3716590 | -4.190781 | 0.0000278 | 0.0004621 | ENSG00000167858.8 | TEKT1 | FC_P | TEKT1 | -1.559638 | 0.0000278 |
| 1.895209e+01 | 1.559634 | 0.3956493 | 3.820144 | 0.0001334 | 0.0015581 | ENSG00000258794.3 | RP11-313F23.5 | FC_P | RP11.313F23.5 | 1.559634 | 0.0001334 |
| 1.201455e+02 | -1.555338 | 0.3456697 | -4.840664 | 0.0000013 | 0.0000407 | ENSG00000093134.9 | VNN3 | FC_P | VNN3 | -1.555338 | 0.0000013 |
| 2.801601e+01 | -1.554479 | 0.3317998 | -4.699404 | 0.0000026 | 0.0000730 | ENSG00000168589.10 | DYNLRB2 | FC_P | DYNLRB2 | -1.554479 | 0.0000026 |
| 8.455202e+00 | -1.554318 | 0.4319698 | -3.476687 | 0.0005077 | 0.0043667 | ENSG00000261713.2 | SSTR5-AS1 | FC_P | SSTR5.AS1 | -1.554318 | 0.0005077 |
| 1.808876e+01 | -1.553342 | 0.3238830 | -4.779411 | 0.0000018 | 0.0000523 | ENSG00000239084.1 | snoU13 | FC_P | snoU13.1 | -1.553342 | 0.0000018 |
| 1.611715e+01 | -1.552972 | 0.3518433 | -4.426809 | 0.0000096 | 0.0002018 | ENSG00000184617.9 | ZNF840 | FC_P | ZNF840 | -1.552972 | 0.0000096 |
| 4.352341e+00 | -1.551216 | 0.4255485 | -3.692417 | 0.0002221 | 0.0023205 | ENSG00000200480.1 | SNORD114-28 | FC_P | SNORD114.28 | -1.551216 | 0.0002221 |
| 9.153142e+01 | 1.551193 | 0.2290808 | 6.707414 | 0.0000000 | 0.0000000 | ENSG00000141965.3 | FEM1A | FC_P | FEM1A | 1.551193 | 0.0000000 |
| 6.582343e+00 | -1.550812 | 0.4198405 | -3.979807 | 0.0000690 | 0.0009366 | ENSG00000206889.1 | RNU6-1200P | FC_P | RNU6.1200P | -1.550812 | 0.0000690 |
| 3.372070e+02 | -1.550550 | 0.3766542 | -4.103474 | 0.0000407 | 0.0006189 | ENSG00000018625.10 | ATP1A2 | FC_P | ATP1A2 | -1.550550 | 0.0000407 |
| 1.618156e+01 | -1.550077 | 0.3671963 | -4.209330 | 0.0000256 | 0.0004327 | ENSG00000255160.1 | RP11-428C19.5 | FC_P | RP11.428C19.5 | -1.550077 | 0.0000256 |
| 6.257576e+01 | -1.548874 | 0.3557593 | -4.323086 | 0.0000154 | 0.0002909 | ENSG00000188993.3 | LRRC66 | FC_P | LRRC66 | -1.548874 | 0.0000154 |
| 4.963583e+01 | -1.547897 | 0.3744388 | -4.510814 | 0.0000065 | 0.0001471 | ENSG00000165078.7 | CPA6 | FC_P | CPA6 | -1.547897 | 0.0000065 |
| 4.597827e+00 | -1.546696 | 0.3739296 | -4.174998 | 0.0000298 | 0.0004876 | ENSG00000228842.2 | PCDH9-AS2 | FC_P | PCDH9.AS2 | -1.546696 | 0.0000298 |
| 3.402624e+00 | -1.545968 | 0.3609463 | -4.219416 | 0.0000245 | 0.0004177 | ENSG00000251722.1 | RNU5E-3P | FC_P | RNU5E.3P | -1.545968 | 0.0000245 |
| 1.592318e+01 | -1.544850 | 0.3712243 | -4.156073 | 0.0000324 | 0.0005176 | ENSG00000255308.1 | RP11-428C19.4 | FC_P | RP11.428C19.4 | -1.544850 | 0.0000324 |
| 5.445472e+00 | -1.544404 | 0.3963451 | -3.992229 | 0.0000655 | 0.0008999 | ENSG00000272958.1 | CMP21-97G8.2 | FC_P | CMP21.97G8.2 | -1.544404 | 0.0000655 |
| 9.734185e+01 | -1.544195 | 0.4137684 | -3.818666 | 0.0001342 | 0.0015650 | ENSG00000108242.8 | CYP2C18 | FC_P | CYP2C18 | -1.544195 | 0.0001342 |
| 1.362036e+01 | -1.542546 | 0.2748294 | -5.607466 | 0.0000000 | 0.0000014 | ENSG00000252294.1 | RNU6-589P | FC_P | RNU6.589P | -1.542546 | 0.0000000 |
| 3.069838e+01 | -1.542401 | 0.2779478 | -5.648466 | 0.0000000 | 0.0000012 | ENSG00000207967.1 | MIR620 | FC_P | MIR620 | -1.542401 | 0.0000000 |
| 2.283738e+01 | -1.538561 | 0.3643478 | -4.249326 | 0.0000214 | 0.0003750 | ENSG00000230062.4 | ANKRD66 | FC_P | ANKRD66 | -1.538561 | 0.0000214 |
| 8.107794e+00 | -1.537181 | 0.3564991 | -4.454194 | 0.0000084 | 0.0001817 | ENSG00000263652.1 | MIR548AX | FC_P | MIR548AX | -1.537181 | 0.0000084 |
| 9.732619e+01 | -1.537131 | 0.3473575 | -4.390701 | 0.0000113 | 0.0002281 | ENSG00000227954.2 | RP3-323P13.2 | FC_P | RP3.323P13.2 | -1.537131 | 0.0000113 |
| 3.673474e+01 | -1.535843 | 0.2572689 | -6.068152 | 0.0000000 | 0.0000002 | ENSG00000207286.1 | Y_RNA | FC_P | Y_RNA.2 | -1.535843 | 0.0000000 |
| 1.056367e+01 | 1.534598 | 0.4376792 | 3.524911 | 0.0004236 | 0.0038063 | ENSG00000227599.1 | RP4-753D4.2 | FC_P | RP4.753D4.2 | 1.534598 | 0.0004236 |
| 1.157003e+01 | 1.534315 | 0.3457975 | 4.402396 | 0.0000107 | 0.0002191 | ENSG00000214784.4 | AC010468.1 | FC_P | AC010468.1 | 1.534315 | 0.0000107 |
| 1.470905e+03 | 1.531104 | 0.4038813 | 4.146028 | 0.0000338 | 0.0005373 | ENSG00000105825.7 | TFPI2 | FC_P | TFPI2 | 1.531104 | 0.0000338 |
| 2.372372e+01 | -1.531027 | 0.3917049 | -3.327857 | 0.0008752 | 0.0066873 | ENSG00000164756.8 | SLC30A8 | FC_P | SLC30A8 | -1.531027 | 0.0008752 |
| 1.126816e+01 | -1.530888 | 0.2796606 | -5.488856 | 0.0000000 | 0.0000025 | ENSG00000252686.1 | RNU6-1234P | FC_P | RNU6.1234P | -1.530888 | 0.0000000 |
| 2.088821e+01 | -1.529041 | 0.3241820 | -4.758227 | 0.0000020 | 0.0000574 | ENSG00000261496.1 | RP13-514E23.1 | FC_P | RP13.514E23.1 | -1.529041 | 0.0000020 |
| 2.019348e+02 | -1.528896 | 0.3570717 | -4.258705 | 0.0000206 | 0.0003615 | ENSG00000197520.6 | FAM177B | FC_P | FAM177B | -1.528896 | 0.0000206 |
| 9.193095e+00 | -1.528844 | 0.4189109 | -3.552773 | 0.0003812 | 0.0035076 | ENSG00000210195.2 | MT-TT | FC_P | MT.TT | -1.528844 | 0.0003812 |
| 6.062482e+00 | -1.526600 | 0.3388602 | -4.489676 | 0.0000071 | 0.0001590 | ENSG00000200508.1 | Y_RNA | FC_P | Y_RNA.3 | -1.526600 | 0.0000071 |
| 9.732164e+01 | 1.524814 | 0.4360688 | 3.339370 | 0.0008397 | 0.0064788 | ENSG00000183242.7 | WT1-AS | FC_P | WT1.AS | 1.524814 | 0.0008397 |
| 2.548883e+00 | -1.523768 | 0.4326909 | -3.582397 | 0.0003405 | 0.0032126 | ENSG00000239184.1 | RNA5SP269 | FC_P | RNA5SP269 | -1.523768 | 0.0003405 |
| 1.434056e+01 | -1.522882 | 0.3702719 | -4.199357 | 0.0000268 | 0.0004485 | ENSG00000254959.2 | INMT-FAM188B | FC_P | INMT.FAM188B | -1.522882 | 0.0000268 |
| 1.113133e+01 | -1.521503 | 0.3217797 | -4.858058 | 0.0000012 | 0.0000381 | ENSG00000238388.1 | snoU13 | FC_P | snoU13.2 | -1.521503 | 0.0000012 |
| 5.203878e+01 | -1.518197 | 0.3754967 | -4.148732 | 0.0000334 | 0.0005315 | ENSG00000229233.1 | AC011891.5 | FC_P | AC011891.5 | -1.518197 | 0.0000334 |
| 5.847675e+00 | -1.517882 | 0.3598884 | -4.384626 | 0.0000116 | 0.0002336 | ENSG00000252210.1 | Y_RNA | FC_P | Y_RNA.4 | -1.517882 | 0.0000116 |
| 4.965776e+00 | 1.517821 | 0.3416592 | 4.413374 | 0.0000102 | 0.0002108 | ENSG00000231977.1 | RP5-963E22.4 | FC_P | RP5.963E22.4 | 1.517821 | 0.0000102 |
| 3.453608e+00 | -1.516391 | 0.4331745 | -3.439144 | 0.0005836 | 0.0048748 | ENSG00000225417.1 | RP5-1178H5.2 | FC_P | RP5.1178H5.2 | -1.516391 | 0.0005836 |
| 2.143091e+00 | -1.516257 | 0.4319315 | -3.384969 | 0.0007119 | 0.0056858 | ENSG00000231720.1 | RP11-568A7.3 | FC_P | RP11.568A7.3 | -1.516257 | 0.0007119 |
| 7.190674e+01 | -1.515836 | 0.3226988 | -4.691450 | 0.0000027 | 0.0000749 | ENSG00000089101.13 | C20orf26 | FC_P | C20orf26 | -1.515836 | 0.0000027 |
| 2.583663e+01 | -1.514908 | 0.2371353 | -6.418420 | 0.0000000 | 0.0000000 | ENSG00000252496.1 | RNA5SP33 | FC_P | RNA5SP33 | -1.514908 | 0.0000000 |
| 2.505869e+01 | -1.514818 | 0.3851561 | -3.905180 | 0.0000942 | 0.0011889 | ENSG00000263429.3 | LINC00675 | FC_P | LINC00675 | -1.514818 | 0.0000942 |
| 1.118913e+01 | -1.514293 | 0.2994027 | -5.009731 | 0.0000005 | 0.0000204 | ENSG00000167355.3 | AC104389.28 | FC_P | AC104389.28 | -1.514293 | 0.0000005 |
| 1.145388e+01 | -1.513706 | 0.3632942 | -4.049824 | 0.0000513 | 0.0007452 | ENSG00000233005.1 | AC067959.1 | FC_P | AC067959.1 | -1.513706 | 0.0000513 |
| 1.016584e+02 | -1.510691 | 0.2915612 | -5.178667 | 0.0000002 | 0.0000100 | ENSG00000197168.7 | NEK5 | FC_P | NEK5 | -1.510691 | 0.0000002 |
| 4.730575e+00 | -1.508917 | 0.4280495 | -3.435003 | 0.0005925 | 0.0049294 | ENSG00000258765.1 | RP11-692C24.2 | FC_P | RP11.692C24.2 | -1.508917 | 0.0005925 |
| 9.642318e+00 | -1.508566 | 0.3672604 | -4.086680 | 0.0000438 | 0.0006550 | ENSG00000242810.1 | MRPL42P6 | FC_P | MRPL42P6 | -1.508566 | 0.0000438 |
| 4.530483e+01 | -1.508454 | 0.4064216 | -3.763919 | 0.0001673 | 0.0018623 | ENSG00000162598.9 | C1orf87 | FC_P | C1orf87 | -1.508454 | 0.0001673 |
| 5.599512e+00 | -1.508323 | 0.3003748 | -4.984584 | 0.0000006 | 0.0000226 | ENSG00000222578.1 | RNA5SP345 | FC_P | RNA5SP345 | -1.508323 | 0.0000006 |
| 1.726251e+00 | -1.506713 | 0.4357671 | -3.528516 | 0.0004179 | 0.0037723 | ENSG00000230258.2 | AC002539.1 | FC_P | AC002539.1 | -1.506713 | 0.0004179 |
| 3.347572e+00 | -1.505292 | 0.3660678 | -4.070770 | 0.0000469 | 0.0006917 | ENSG00000242180.2 | OR51B5 | FC_P | OR51B5 | -1.505292 | 0.0000469 |
| 3.816121e+00 | -1.505219 | 0.3516150 | -4.263974 | 0.0000201 | 0.0003557 | ENSG00000273389.1 | RP13-514E23.2 | FC_P | RP13.514E23.2 | -1.505219 | 0.0000201 |
| 5.342284e+00 | -1.504836 | 0.3511695 | -4.359477 | 0.0000130 | 0.0002569 | ENSG00000207267.1 | RNU6-1081P | FC_P | RNU6.1081P | -1.504836 | 0.0000130 |
| 5.959016e+00 | -1.504820 | 0.3902608 | -3.812581 | 0.0001375 | 0.0015985 | ENSG00000258162.1 | RP11-315E17.1 | FC_P | RP11.315E17.1 | -1.504820 | 0.0001375 |
| 8.870222e+01 | -1.502227 | 0.3206199 | -4.729730 | 0.0000022 | 0.0000644 | ENSG00000166596.10 | WDR16 | FC_P | WDR16 | -1.502227 | 0.0000022 |
Pathway enrichment analysis fGSEA
Low BAP1 is the reference. When BAP1 is high, pathways shown below are up- or down- regulated
fgsea_res <- fgsea_analysis(DE_res)## `summarise()` ungrouping output (override with `.groups` argument)## Warning in fgsea(pathways = gmtPathways(pthw_path), stats = ranks, nperm = 1000): There are ties in the preranked stats (0.05% of the list).
## The order of those tied genes will be arbitrary, which may produce unexpected results.
## Warning in fgsea(pathways = gmtPathways(pthw_path), stats = ranks, nperm = 1000): There are ties in the preranked stats (0.05% of the list).
## The order of those tied genes will be arbitrary, which may produce unexpected results.
## Warning in fgsea(pathways = gmtPathways(pthw_path), stats = ranks, nperm = 1000): There are ties in the preranked stats (0.05% of the list).
## The order of those tied genes will be arbitrary, which may produce unexpected results.
## Warning in fgsea(pathways = gmtPathways(pthw_path), stats = ranks, nperm = 1000): There are ties in the preranked stats (0.05% of the list).
## The order of those tied genes will be arbitrary, which may produce unexpected results.
## Warning in fgsea(pathways = gmtPathways(pthw_path), stats = ranks, nperm = 1000): There are ties in the preranked stats (0.05% of the list).
## The order of those tied genes will be arbitrary, which may produce unexpected results.
## Warning in fgsea(pathways = gmtPathways(pthw_path), stats = ranks, nperm = 1000): There are ties in the preranked stats (0.05% of the list).
## The order of those tied genes will be arbitrary, which may produce unexpected results.
## Warning in fgsea(pathways = gmtPathways(pthw_path), stats = ranks, nperm = 1000): There are ties in the preranked stats (0.05% of the list).
## The order of those tied genes will be arbitrary, which may produce unexpected results.
## Warning in fgsea(pathways = gmtPathways(pthw_path), stats = ranks, nperm = 1000): There are ties in the preranked stats (0.05% of the list).
## The order of those tied genes will be arbitrary, which may produce unexpected results.
## Warning in fgsea(pathways = gmtPathways(pthw_path), stats = ranks, nperm = 1000): There are ties in the preranked stats (0.05% of the list).
## The order of those tied genes will be arbitrary, which may produce unexpected results.fgp <- fgsea_plot(fgsea_res$res_hm, pathways_title='Hallmark', condition_name='BAP1 low vs high')
kable(fgp)| pathway | pval | padj | ES | NES | nMoreExtreme | size | state |
|---|---|---|---|---|---|---|---|
| HALLMARK_MYC_TARGETS_V2 | 0.0019841 | 0.0031048 | 0.7514702 | 2.985838 | 0 | 57 | up |
| HALLMARK_MYC_TARGETS_V1 | 0.0019120 | 0.0031048 | 0.5951325 | 2.882789 | 0 | 189 | up |
| HALLMARK_DNA_REPAIR | 0.0018587 | 0.0031048 | 0.5669329 | 2.639105 | 0 | 141 | up |
| HALLMARK_REACTIVE_OXYGEN_SPECIES_PATHWAY | 0.0019920 | 0.0031048 | 0.6926141 | 2.626220 | 0 | 46 | up |
| HALLMARK_P53_PATHWAY | 0.0018975 | 0.0031048 | 0.5354251 | 2.595026 | 0 | 190 | up |
| HALLMARK_G2M_CHECKPOINT | 0.0019120 | 0.0031048 | 0.5121996 | 2.478671 | 0 | 187 | up |
| HALLMARK_UNFOLDED_PROTEIN_RESPONSE | 0.0019569 | 0.0031048 | 0.5601328 | 2.470739 | 0 | 103 | up |
| HALLMARK_E2F_TARGETS | 0.0019084 | 0.0031048 | 0.5029007 | 2.432800 | 0 | 191 | up |
| HALLMARK_UV_RESPONSE_UP | 0.0018484 | 0.0031048 | 0.5152321 | 2.422013 | 0 | 147 | up |
| HALLMARK_MITOTIC_SPINDLE | 0.0018797 | 0.0031048 | 0.4951850 | 2.409677 | 0 | 195 | up |
| HALLMARK_OXIDATIVE_PHOSPHORYLATION | 0.0018939 | 0.0031048 | 0.4960800 | 2.384563 | 0 | 175 | up |
| HALLMARK_TNFA_SIGNALING_VIA_NFKB | 0.0018797 | 0.0031048 | 0.4853719 | 2.361925 | 0 | 195 | up |
| HALLMARK_INTERFERON_ALPHA_RESPONSE | 0.0019417 | 0.0031048 | 0.5260215 | 2.295795 | 0 | 93 | up |
| HALLMARK_PI3K_AKT_MTOR_SIGNALING | 0.0019569 | 0.0031048 | 0.5143544 | 2.268811 | 0 | 103 | up |
| HALLMARK_INTERFERON_GAMMA_RESPONSE | 0.0018868 | 0.0031048 | 0.4644912 | 2.256368 | 0 | 194 | up |
| HALLMARK_MTORC1_SIGNALING | 0.0018975 | 0.0031048 | 0.4637870 | 2.247821 | 0 | 190 | up |
| HALLMARK_APOPTOSIS | 0.0018519 | 0.0031048 | 0.4714723 | 2.227226 | 0 | 155 | up |
| HALLMARK_GLYCOLYSIS | 0.0019120 | 0.0031048 | 0.4162795 | 2.014886 | 0 | 188 | up |
| HALLMARK_APICAL_JUNCTION | 0.0019120 | 0.0031048 | 0.4133881 | 2.002429 | 0 | 189 | up |
| HALLMARK_ALLOGRAFT_REJECTION | 0.0019120 | 0.0031048 | 0.4081824 | 1.975304 | 0 | 187 | up |
| HALLMARK_ADIPOGENESIS | 0.0019084 | 0.0031048 | 0.4086975 | 1.969521 | 0 | 183 | up |
| HALLMARK_WNT_BETA_CATENIN_SIGNALING | 0.0020408 | 0.0031048 | 0.5188031 | 1.923844 | 0 | 42 | up |
| HALLMARK_INFLAMMATORY_RESPONSE | 0.0018868 | 0.0031048 | 0.3906481 | 1.897625 | 0 | 193 | up |
| HALLMARK_MYOGENESIS | 0.0018975 | 0.0031048 | 0.3863939 | 1.872722 | 0 | 190 | up |
| HALLMARK_IL6_JAK_STAT3_SIGNALING | 0.0020492 | 0.0031048 | 0.4396043 | 1.859896 | 0 | 82 | up |
| HALLMARK_ESTROGEN_RESPONSE_LATE | 0.0018868 | 0.0031048 | 0.3751503 | 1.822342 | 0 | 193 | up |
| HALLMARK_CHOLESTEROL_HOMEOSTASIS | 0.0019724 | 0.0031048 | 0.4383596 | 1.811611 | 0 | 69 | up |
| HALLMARK_HEME_METABOLISM | 0.0019194 | 0.0031048 | 0.3709272 | 1.782191 | 0 | 179 | up |
| HALLMARK_ESTROGEN_RESPONSE_EARLY | 0.0019084 | 0.0031048 | 0.3670963 | 1.775841 | 0 | 191 | up |
| HALLMARK_HYPOXIA | 0.0019048 | 0.0031048 | 0.3686240 | 1.771905 | 0 | 180 | up |
fgp <- fgsea_plot(fgsea_res$res_c1, pathways_title='C1 positional genes', condition_name='BAP1 low vs high')
kable(fgp)| pathway | pval | padj | ES | NES | nMoreExtreme | size | state |
|---|---|---|---|---|---|---|---|
| chr19p13 | 0.0018657 | 0.0059037 | 0.7507847 | 4.048989 | 0 | 544 | up |
| chr9q34 | 0.0018553 | 0.0059037 | 0.7295889 | 3.578502 | 0 | 210 | up |
| chr17q25 | 0.0018762 | 0.0059037 | 0.6672525 | 3.260381 | 0 | 202 | up |
| chr3p21 | 0.0018657 | 0.0059037 | 0.6541574 | 3.210588 | 0 | 211 | up |
| chr19q13 | 0.0018149 | 0.0059037 | 0.5602329 | 3.098032 | 0 | 769 | up |
| chr16p11 | 0.0019157 | 0.0059037 | 0.6603864 | 3.012990 | 0 | 120 | up |
| chr11q13 | 0.0018450 | 0.0059037 | 0.5918730 | 3.009112 | 0 | 290 | up |
| chr16q24 | 0.0020040 | 0.0059037 | 0.6331231 | 2.733117 | 0 | 92 | up |
| chr1p31 | 0.0020833 | 0.0059037 | -0.5831812 | -2.646177 | 0 | 120 | down |
| chr7p22 | 0.0020325 | 0.0059037 | 0.6055466 | 2.592822 | 0 | 85 | up |
| chr4p16 | 0.0019194 | 0.0059037 | 0.5684632 | 2.582216 | 0 | 118 | up |
| chr22q13 | 0.0018762 | 0.0059037 | 0.5237570 | 2.573764 | 0 | 215 | up |
| chr1q22 | 0.0020790 | 0.0059037 | 0.6570445 | 2.547734 | 0 | 53 | up |
| chr17p13 | 0.0018149 | 0.0059037 | 0.5034765 | 2.512875 | 0 | 236 | up |
| chr7q36 | 0.0019920 | 0.0059037 | 0.5704783 | 2.511936 | 0 | 101 | up |
| chr20q11 | 0.0019724 | 0.0059037 | 0.5282767 | 2.489806 | 0 | 159 | up |
| chr17q21 | 0.0018450 | 0.0059037 | 0.4838084 | 2.440629 | 0 | 271 | up |
| chr12q21 | 0.0019685 | 0.0059037 | -0.5970674 | -2.440323 | 0 | 66 | down |
| chr20q13 | 0.0018382 | 0.0059037 | 0.4797197 | 2.416472 | 0 | 265 | up |
| chr12p12 | 0.0019455 | 0.0059037 | -0.5717705 | -2.331402 | 0 | 65 | down |
| chr7q22 | 0.0019724 | 0.0059037 | 0.4965144 | 2.329010 | 0 | 153 | up |
| chr5q35 | 0.0019380 | 0.0059037 | 0.5031428 | 2.328435 | 0 | 135 | up |
| chr9p13 | 0.0018939 | 0.0059037 | 0.5079495 | 2.301112 | 0 | 113 | up |
| chr5p13 | 0.0019455 | 0.0059037 | -0.5355983 | -2.298951 | 0 | 84 | down |
| chr12q24 | 0.0018587 | 0.0059037 | 0.4558662 | 2.279257 | 0 | 250 | up |
| chr1q21 | 0.0018762 | 0.0059037 | 0.4685764 | 2.275820 | 0 | 191 | up |
| chr8q21 | 0.0019960 | 0.0059037 | -0.5192316 | -2.250271 | 0 | 90 | down |
| chr8q22 | 0.0019455 | 0.0059037 | -0.5240361 | -2.249322 | 0 | 84 | down |
| chr22q11 | 0.0018868 | 0.0059037 | 0.4528396 | 2.220897 | 0 | 214 | up |
| chr16p13 | 0.0018282 | 0.0059037 | 0.4379570 | 2.213789 | 0 | 272 | up |
fgp <- fgsea_plot(fgsea_res$res_c2, pathways_title='C2 curated genes', condition_name='BAP1 low vs high')
kable(fgp)| pathway | pval | padj | ES | NES | nMoreExtreme | size | state |
|---|---|---|---|---|---|---|---|
| GINESTIER_BREAST_CANCER_ZNF217_AMPLIFIED_DN | 0.0019802 | 0.0079622 | 0.7426209 | 3.761729 | 0 | 308 | up |
| LU_EZH2_TARGETS_UP | 0.0019194 | 0.0079622 | 0.6838918 | 3.395229 | 0 | 257 | up |
| SPIELMAN_LYMPHOBLAST_EUROPEAN_VS_ASIAN_UP | 0.0018832 | 0.0079622 | 0.6407552 | 3.372171 | 0 | 444 | up |
| RICKMAN_METASTASIS_DN | 0.0019305 | 0.0079622 | 0.6842922 | 3.371849 | 0 | 246 | up |
| MARTENS_TRETINOIN_RESPONSE_DN | 0.0018182 | 0.0079622 | 0.6052181 | 3.357854 | 0 | 722 | up |
| MARTENS_BOUND_BY_PML_RARA_FUSION | 0.0019493 | 0.0079622 | 0.6332474 | 3.307524 | 0 | 418 | up |
| REACTOME_RRNA_PROCESSING | 0.0019305 | 0.0079622 | 0.6887952 | 3.285542 | 0 | 184 | up |
| DACOSTA_UV_RESPONSE_VIA_ERCC3_UP | 0.0019342 | 0.0079622 | 0.6484617 | 3.278440 | 0 | 294 | up |
| KIM_ALL_DISORDERS_OLIGODENDROCYTE_NUMBER_CORR_UP | 0.0018519 | 0.0079622 | 0.5935414 | 3.275786 | 0 | 693 | up |
| WELCSH_BRCA1_TARGETS_DN | 0.0019608 | 0.0079622 | 0.7266808 | 3.247569 | 0 | 127 | up |
| ENK_UV_RESPONSE_KERATINOCYTE_UP | 0.0018484 | 0.0079622 | 0.6087051 | 3.238186 | 0 | 487 | up |
| KIM_ALL_DISORDERS_DURATION_CORR_DN | 0.0019569 | 0.0079622 | 0.7124291 | 3.230082 | 0 | 134 | up |
| REACTOME_EUKARYOTIC_TRANSLATION_ELONGATION | 0.0020040 | 0.0079622 | 0.7715309 | 3.228295 | 0 | 86 | up |
| REACTOME_EUKARYOTIC_TRANSLATION_INITIATION | 0.0019531 | 0.0079622 | 0.7426040 | 3.227236 | 0 | 112 | up |
| HSIAO_HOUSEKEEPING_GENES | 0.0019231 | 0.0079622 | 0.6232810 | 3.213668 | 0 | 362 | up |
| SANSOM_APC_TARGETS_REQUIRE_MYC | 0.0019960 | 0.0079622 | 0.6661419 | 3.211729 | 0 | 209 | up |
| KEGG_RIBOSOME | 0.0020121 | 0.0079622 | 0.7683390 | 3.197411 | 0 | 81 | up |
| SCHLOSSER_SERUM_RESPONSE_AUGMENTED_BY_MYC | 0.0019608 | 0.0079622 | 0.7394982 | 3.183014 | 0 | 101 | up |
| LI_DCP2_BOUND_MRNA | 0.0020080 | 0.0079622 | 0.7644617 | 3.165287 | 0 | 78 | up |
| REACTOME_INFLUENZA_INFECTION | 0.0019646 | 0.0079622 | 0.6891440 | 3.159990 | 0 | 145 | up |
| REACTOME_NONSENSE_MEDIATED_DECAY_NMD | 0.0019685 | 0.0079622 | 0.7298401 | 3.151569 | 0 | 108 | up |
| REACTOME_METABOLISM_OF_RNA | 0.0018975 | 0.0079622 | 0.5721733 | 3.120585 | 0 | 626 | up |
| REACTOME_TRANSLATION | 0.0019194 | 0.0079622 | 0.6252563 | 3.108811 | 0 | 262 | up |
| REACTOME_RESPONSE_OF_EIF2AK4_GCN2_TO_AMINO_ACID_DEFICIENCY | 0.0019646 | 0.0079622 | 0.7258810 | 3.084952 | 0 | 94 | up |
| REACTOME_SELENOAMINO_ACID_METABOLISM | 0.0019685 | 0.0079622 | 0.7129670 | 3.068063 | 0 | 102 | up |
| KASLER_HDAC7_TARGETS_1_UP | 0.0019157 | 0.0079622 | 0.6493167 | 3.067242 | 0 | 168 | up |
| AMIT_EGF_RESPONSE_480_HELA | 0.0019685 | 0.0079622 | 0.6600758 | 3.051282 | 0 | 151 | up |
| LOPEZ_MBD_TARGETS | 0.0017857 | 0.0079622 | 0.5425486 | 3.048602 | 0 | 885 | up |
| CAIRO_HEPATOBLASTOMA_CLASSES_UP | 0.0018587 | 0.0079622 | 0.5635591 | 3.046571 | 0 | 560 | up |
| SANSOM_APC_MYC_TARGETS | 0.0019531 | 0.0079622 | 0.6241811 | 3.035292 | 0 | 224 | up |
fgp <- fgsea_plot(fgsea_res$res_c3, pathways_title='C3 regulatory target genes', condition_name='BAP1 low vs high')
kable(fgp)| pathway | pval | padj | ES | NES | nMoreExtreme | size | state |
|---|---|---|---|---|---|---|---|
| SUPT20H_TARGET_GENES | 0.0018587 | 0.0067637 | 0.5587984 | 3.191683 | 0 | 1169 | up |
| CEBPZ_TARGET_GENES | 0.0018116 | 0.0067637 | 0.5487399 | 3.162717 | 0 | 1304 | up |
| HDGF_TARGET_GENES | 0.0018939 | 0.0067637 | 0.5645479 | 3.132154 | 0 | 776 | up |
| SETD7_TARGET_GENES | 0.0018868 | 0.0067637 | 0.5641538 | 3.130648 | 0 | 786 | up |
| MIR4492 | 0.0018832 | 0.0067637 | 0.5958888 | 3.110372 | 0 | 372 | up |
| ZNF436_TARGET_GENES | 0.0019157 | 0.0067637 | 0.5883892 | 3.105689 | 0 | 429 | up |
| FXR1_TARGET_GENES | 0.0018553 | 0.0067637 | 0.5482645 | 3.098145 | 0 | 1002 | up |
| NFKBIA_TARGET_GENES | 0.0018051 | 0.0067637 | 0.5457988 | 3.095049 | 0 | 1011 | up |
| MIR4283 | 0.0019417 | 0.0067637 | 0.6330661 | 3.051605 | 0 | 194 | up |
| MIR6825_5P | 0.0019011 | 0.0067637 | 0.5845721 | 3.051434 | 0 | 379 | up |
| THAP1_TARGET_GENES | 0.0018832 | 0.0067637 | 0.5222676 | 3.041789 | 0 | 1667 | up |
| ADNP_TARGET_GENES | 0.0018622 | 0.0067637 | 0.5587294 | 3.033462 | 0 | 543 | up |
| KLF14_TARGET_GENES | 0.0019268 | 0.0067637 | 0.6176392 | 3.030428 | 0 | 215 | up |
| MIR4763_3P | 0.0019531 | 0.0067637 | 0.6142792 | 3.029706 | 0 | 225 | up |
| RBM34_TARGET_GENES | 0.0018519 | 0.0067637 | 0.5396694 | 3.015813 | 0 | 846 | up |
| MIR4731_5P | 0.0019048 | 0.0067637 | 0.6012254 | 2.992164 | 0 | 237 | up |
| KAT5_TARGET_GENES | 0.0018622 | 0.0067637 | 0.5386702 | 2.990838 | 0 | 768 | up |
| MIR1207_5P | 0.0018553 | 0.0067637 | 0.5815773 | 2.966539 | 0 | 301 | up |
| EPC1_TARGET_GENES | 0.0019048 | 0.0067637 | 0.5730291 | 2.952376 | 0 | 332 | up |
| KLF13_TARGET_GENES | 0.0018692 | 0.0067637 | 0.5059913 | 2.952132 | 0 | 1766 | up |
| MIR486_3P | 0.0019455 | 0.0067637 | 0.6396048 | 2.950824 | 0 | 153 | up |
| MCM2_TARGET_GENES | 0.0020202 | 0.0067637 | 0.7176487 | 2.941038 | 0 | 76 | up |
| CIITA_TARGET_GENES | 0.0018315 | 0.0067637 | 0.5172643 | 2.936420 | 0 | 1039 | up |
| MIR4505 | 0.0019380 | 0.0067637 | 0.5921316 | 2.936374 | 0 | 235 | up |
| MIR423_5P | 0.0019231 | 0.0067637 | 0.6522103 | 2.934732 | 0 | 129 | up |
| CDC73_TARGET_GENES | 0.0018762 | 0.0067637 | 0.5417707 | 2.933345 | 0 | 538 | up |
| MIR6721_5P | 0.0018484 | 0.0067637 | 0.5723532 | 2.925491 | 0 | 308 | up |
| ZNF92_TARGET_GENES | 0.0018727 | 0.0067637 | 0.5109499 | 2.920817 | 0 | 1183 | up |
| JDP2_TARGET_GENES | 0.0018484 | 0.0067637 | 0.4999463 | 2.915312 | 0 | 1661 | up |
| MIR6883_5P | 0.0018975 | 0.0067637 | 0.5551820 | 2.897276 | 0 | 380 | up |
fgp <- fgsea_plot(fgsea_res$res_c4, pathways_title='C4 cancer', condition_name='BAP1 low vs high')
kable(fgp)| pathway | pval | padj | ES | NES | nMoreExtreme | size | state |
|---|---|---|---|---|---|---|---|
| MORF_UBE2I | 0.0019493 | 0.0051258 | 0.7133588 | 3.527450 | 0 | 219 | up |
| MORF_PHB | 0.0019120 | 0.0051258 | 0.7680946 | 3.476173 | 0 | 113 | up |
| MORF_NME2 | 0.0019342 | 0.0051258 | 0.7289640 | 3.408664 | 0 | 141 | up |
| MORF_NPM1 | 0.0019608 | 0.0051258 | 0.7185991 | 3.381004 | 0 | 149 | up |
| MORF_CSNK2B | 0.0018832 | 0.0051258 | 0.6701245 | 3.380885 | 0 | 258 | up |
| MORF_ACTG1 | 0.0019380 | 0.0051258 | 0.7308713 | 3.366872 | 0 | 127 | up |
| MORF_AP2M1 | 0.0019194 | 0.0051258 | 0.6851841 | 3.362316 | 0 | 203 | up |
| MORF_ANP32B | 0.0020161 | 0.0051258 | 0.6985141 | 3.358730 | 0 | 183 | up |
| MORF_AATF | 0.0019802 | 0.0051258 | 0.6924533 | 3.357759 | 0 | 191 | up |
| MORF_FBL | 0.0019194 | 0.0051258 | 0.7240208 | 3.345283 | 0 | 129 | up |
| MORF_RAD23A | 0.0018622 | 0.0051258 | 0.6429129 | 3.318616 | 0 | 304 | up |
| MORF_DDB1 | 0.0019268 | 0.0051258 | 0.6666799 | 3.308989 | 0 | 226 | up |
| MORF_EIF3S2 | 0.0019417 | 0.0051258 | 0.6676889 | 3.306004 | 0 | 220 | up |
| MORF_TPT1 | 0.0019531 | 0.0051258 | 0.7594675 | 3.305835 | 0 | 92 | up |
| MORF_MAP2K2 | 0.0019531 | 0.0051258 | 0.7265419 | 3.292324 | 0 | 117 | up |
| MORF_IKBKG | 0.0019493 | 0.0051258 | 0.7139560 | 3.283910 | 0 | 126 | up |
| MORF_DAP3 | 0.0020243 | 0.0051258 | 0.6815812 | 3.274829 | 0 | 179 | up |
| MORF_RAN | 0.0019157 | 0.0051258 | 0.6511978 | 3.254191 | 0 | 239 | up |
| MORF_RPA2 | 0.0020161 | 0.0051258 | 0.6793347 | 3.253192 | 0 | 176 | up |
| GNF2_EIF3S6 | 0.0019194 | 0.0051258 | 0.7163001 | 3.228532 | 0 | 110 | up |
| MORF_BUB3 | 0.0019194 | 0.0051258 | 0.6462123 | 3.226195 | 0 | 243 | up |
| GCM_CSNK2B | 0.0019531 | 0.0051258 | 0.7497331 | 3.214405 | 0 | 87 | up |
| MODULE_83 | 0.0018622 | 0.0051258 | 0.6244084 | 3.199685 | 0 | 290 | up |
| MORF_HDAC1 | 0.0019048 | 0.0051258 | 0.6413447 | 3.197034 | 0 | 231 | up |
| GCM_TPT1 | 0.0020202 | 0.0051258 | 0.7992662 | 3.166444 | 0 | 59 | up |
| MORF_CTBP1 | 0.0020000 | 0.0051258 | 0.6673619 | 3.164312 | 0 | 159 | up |
| MODULE_257 | 0.0019724 | 0.0051258 | 0.6704206 | 3.155993 | 0 | 150 | up |
| MORF_PPP1CA | 0.0020161 | 0.0051258 | 0.6665923 | 3.141889 | 0 | 153 | up |
| MORF_G22P1 | 0.0020243 | 0.0051258 | 0.6599471 | 3.124111 | 0 | 158 | up |
| MORF_GNB1 | 0.0018832 | 0.0051258 | 0.6137062 | 3.123175 | 0 | 274 | up |
fgp <- fgsea_plot(fgsea_res$res_c5, pathways_title='C5 GO genes', condition_name='BAP1 low vs high')
kable(fgp)| pathway | pval | padj | ES | NES | nMoreExtreme | size | state |
|---|---|---|---|---|---|---|---|
| GO_VIRAL_GENE_EXPRESSION | 0.0019685 | 0.0101779 | 0.7022003 | 3.368700 | 0 | 185 | up |
| GO_NUCLEAR_TRANSCRIBED_MRNA_CATABOLIC_PROCESS_NONSENSE_MEDIATED_DECAY | 0.0019802 | 0.0101779 | 0.7260161 | 3.245483 | 0 | 114 | up |
| GO_RIBOSOME_BIOGENESIS | 0.0020534 | 0.0101779 | 0.6381337 | 3.200949 | 0 | 259 | up |
| GO_STRUCTURAL_CONSTITUENT_OF_RIBOSOME | 0.0020284 | 0.0101779 | 0.6778943 | 3.163143 | 0 | 152 | up |
| GO_TRANSLATIONAL_INITIATION | 0.0019920 | 0.0101779 | 0.6601471 | 3.149390 | 0 | 179 | up |
| GO_RIBONUCLEOPROTEIN_COMPLEX | 0.0019531 | 0.0101779 | 0.5721550 | 3.144505 | 0 | 630 | up |
| GO_RIBOSOMAL_SUBUNIT | 0.0020040 | 0.0101779 | 0.6578464 | 3.128156 | 0 | 172 | up |
| GO_CYTOSOLIC_RIBOSOME | 0.0019157 | 0.0101779 | 0.7178149 | 3.109921 | 0 | 95 | up |
| GO_RIBONUCLEOPROTEIN_COMPLEX_BIOGENESIS | 0.0019646 | 0.0101779 | 0.5908406 | 3.099263 | 0 | 382 | up |
| GO_LARGE_RIBOSOMAL_SUBUNIT | 0.0019960 | 0.0101779 | 0.7027448 | 3.096872 | 0 | 108 | up |
| GO_CYTOSOLIC_LARGE_RIBOSOMAL_SUBUNIT | 0.0020619 | 0.0101779 | 0.8017296 | 3.086059 | 0 | 53 | up |
| GO_COTRANSLATIONAL_PROTEIN_TARGETING_TO_MEMBRANE | 0.0019493 | 0.0101779 | 0.7162438 | 3.082829 | 0 | 94 | up |
| GO_RIBOSOMAL_LARGE_SUBUNIT_BIOGENESIS | 0.0019920 | 0.0101779 | 0.7665020 | 3.077570 | 0 | 62 | up |
| GO_RIBOSOME | 0.0019841 | 0.0101779 | 0.6254103 | 3.050640 | 0 | 211 | up |
| GO_ESTABLISHMENT_OF_PROTEIN_LOCALIZATION_TO_ENDOPLASMIC_RETICULUM | 0.0019417 | 0.0101779 | 0.6894414 | 3.039172 | 0 | 106 | up |
| GO_RRNA_METABOLIC_PROCESS | 0.0020000 | 0.0101779 | 0.6305050 | 3.028541 | 0 | 195 | up |
| GO_PROTEIN_TARGETING_TO_MEMBRANE | 0.0020040 | 0.0101779 | 0.6273435 | 2.987217 | 0 | 173 | up |
| GO_NUCLEAR_TRANSCRIBED_MRNA_CATABOLIC_PROCESS | 0.0020080 | 0.0101779 | 0.6203842 | 2.964279 | 0 | 189 | up |
| GO_INTERSPECIES_INTERACTION_BETWEEN_ORGANISMS | 0.0019194 | 0.0101779 | 0.5279694 | 2.959300 | 0 | 859 | up |
| GO_ESTABLISHMENT_OF_PROTEIN_LOCALIZATION_TO_MEMBRANE | 0.0019646 | 0.0101779 | 0.5770295 | 2.956024 | 0 | 296 | up |
| GO_NUCLEOLUS | 0.0018622 | 0.0101779 | 0.5254808 | 2.944526 | 0 | 837 | up |
| GO_PRERIBOSOME | 0.0019841 | 0.0101779 | 0.7164599 | 2.937476 | 0 | 71 | up |
| GO_PROTEIN_LOCALIZATION_TO_ENDOPLASMIC_RETICULUM | 0.0019531 | 0.0101779 | 0.6456861 | 2.929843 | 0 | 128 | up |
| GO_MRNA_METABOLIC_PROCESS | 0.0019231 | 0.0101779 | 0.5267203 | 2.924927 | 0 | 763 | up |
| GO_NCRNA_PROCESSING | 0.0020121 | 0.0101779 | 0.5697821 | 2.924319 | 0 | 325 | up |
| GO_RNA_BINDING | 0.0018215 | 0.0101779 | 0.5049426 | 2.917848 | 0 | 1578 | up |
| GO_RNA_PROCESSING | 0.0018762 | 0.0101779 | 0.5186190 | 2.902894 | 0 | 817 | up |
| GO_RIBOSOME_ASSEMBLY | 0.0020325 | 0.0101779 | 0.7522069 | 2.899366 | 0 | 52 | up |
| GO_RNA_CATABOLIC_PROCESS | 0.0020243 | 0.0101779 | 0.5520966 | 2.878377 | 0 | 366 | up |
| GO_NCRNA_METABOLIC_PROCESS | 0.0020040 | 0.0101779 | 0.5451428 | 2.856717 | 0 | 396 | up |
fgp <- fgsea_plot(fgsea_res$res_c6, pathways_title='C6 oncogenic', condition_name='BAP1 low vs high')
kable(fgp)| pathway | pval | padj | ES | NES | nMoreExtreme | size | state |
|---|---|---|---|---|---|---|---|
| PRC2_EED_UP.V1_DN | 0.0019608 | 0.0057851 | 0.6632460 | 3.169888 | 0 | 179 | up |
| PDGF_ERK_DN.V1_DN | 0.0019608 | 0.0057851 | 0.6401067 | 2.957151 | 0 | 141 | up |
| MYC_UP.V1_UP | 0.0019920 | 0.0057851 | 0.6054549 | 2.834592 | 0 | 157 | up |
| CYCLIN_D1_UP.V1_UP | 0.0019881 | 0.0057851 | 0.5709890 | 2.714571 | 0 | 173 | up |
| CAMP_UP.V1_UP | 0.0019724 | 0.0057851 | 0.5519773 | 2.635868 | 0 | 181 | up |
| RB_P130_DN.V1_UP | 0.0019569 | 0.0057851 | 0.5636551 | 2.522018 | 0 | 114 | up |
| CYCLIN_D1_KE_.V1_UP | 0.0019802 | 0.0057851 | 0.5280465 | 2.518532 | 0 | 178 | up |
| RAPA_EARLY_UP.V1_DN | 0.0019841 | 0.0057851 | 0.5303480 | 2.507278 | 0 | 167 | up |
| IL15_UP.V1_UP | 0.0020040 | 0.0057851 | 0.5262108 | 2.502848 | 0 | 174 | up |
| SRC_UP.V1_UP | 0.0019380 | 0.0057851 | 0.5332113 | 2.480464 | 0 | 148 | up |
| E2F1_UP.V1_UP | 0.0019881 | 0.0057851 | 0.5208068 | 2.475997 | 0 | 173 | up |
| ATF2_UP.V1_UP | 0.0019881 | 0.0057851 | 0.5151452 | 2.429911 | 0 | 165 | up |
| ESC_J1_UP_EARLY.V1_DN | 0.0019960 | 0.0057851 | 0.5213551 | 2.422574 | 0 | 153 | up |
| RB_DN.V1_UP | 0.0019011 | 0.0057851 | 0.5254773 | 2.389480 | 0 | 123 | up |
| PIGF_UP.V1_DN | 0.0019724 | 0.0057851 | 0.5008974 | 2.380663 | 0 | 169 | up |
| RB_P107_DN.V1_UP | 0.0019268 | 0.0057851 | 0.5214990 | 2.376944 | 0 | 128 | up |
| SIRNA_EIF4GI_UP | 0.0019920 | 0.0057851 | 0.5477723 | 2.345644 | 0 | 87 | up |
| RPS14_DN.V1_DN | 0.0019841 | 0.0057851 | 0.4911143 | 2.335902 | 0 | 172 | up |
| IL2_UP.V1_UP | 0.0019802 | 0.0057851 | 0.4751610 | 2.255889 | 0 | 170 | up |
| CSR_LATE_UP.V1_UP | 0.0019763 | 0.0057851 | 0.4796270 | 2.243683 | 0 | 156 | up |
| GCNP_SHH_UP_LATE.V1_DN | 0.0019841 | 0.0057851 | 0.4743939 | 2.242749 | 0 | 167 | up |
| ESC_V6.5_UP_EARLY.V1_UP | 0.0019960 | 0.0057851 | 0.4804199 | 2.229788 | 0 | 152 | up |
| ESC_V6.5_UP_LATE.V1_DN | 0.0019881 | 0.0057851 | 0.4684776 | 2.209783 | 0 | 165 | up |
| MEL18_DN.V1_UP | 0.0019417 | 0.0057851 | 0.4837492 | 2.201524 | 0 | 129 | up |
| ESC_J1_UP_LATE.V1_DN | 0.0020040 | 0.0057851 | 0.4613903 | 2.194538 | 0 | 174 | up |
| CSR_EARLY_UP.V1_UP | 0.0019455 | 0.0057851 | 0.4704720 | 2.165972 | 0 | 139 | up |
| BCAT_BILD_ET_AL_UP | 0.0019960 | 0.0057851 | 0.5827447 | 2.155810 | 0 | 43 | up |
| CRX_NRL_DN.V1_UP | 0.0019011 | 0.0057851 | 0.4696732 | 2.135724 | 0 | 123 | up |
| AKT_UP_MTOR_DN.V1_UP | 0.0020040 | 0.0057851 | 0.4472208 | 2.109560 | 0 | 166 | up |
| RAPA_EARLY_UP.V1_UP | 0.0019048 | 0.0057851 | 0.4518858 | 2.105253 | 0 | 146 | up |
fgp <- fgsea_plot(fgsea_res$res_c7, pathways_title='C7 immunologic', condition_name='BAP1 low vs high')
kable(fgp)| pathway | pval | padj | ES | NES | nMoreExtreme | size | state |
|---|---|---|---|---|---|---|---|
| GSE9006_TYPE_1_VS_TYPE_2_DIABETES_PBMC_AT_DX_UP | 0.0018939 | 0.0027001 | 0.8136341 | 3.968296 | 0 | 187 | up |
| GSE9006_HEALTHY_VS_TYPE_2_DIABETES_PBMC_AT_DX_UP | 0.0019084 | 0.0027001 | 0.7489666 | 3.647362 | 0 | 181 | up |
| GSE16385_MONOCYTE_VS_12H_IL4_TREATED_MACROPHAGE_DN | 0.0018553 | 0.0027001 | 0.7370112 | 3.608971 | 0 | 183 | up |
| GSE45837_WT_VS_GFI1_KO_PDC_DN | 0.0019194 | 0.0027001 | 0.7381046 | 3.594444 | 0 | 180 | up |
| GSE369_PRE_VS_POST_IL6_INJECTION_SOCS3_KO_LIVER_DN | 0.0018939 | 0.0027001 | 0.7339672 | 3.579741 | 0 | 187 | up |
| GSE9601_UNTREATED_VS_PI3K_INHIBITOR_TREATED_HCMV_INF_MONOCYTE_UP | 0.0019268 | 0.0027001 | 0.7267557 | 3.484145 | 0 | 162 | up |
| GSE36527_CD69_NEG_VS_POS_TREG_CD62L_LOS_KLRG1_NEG_DN | 0.0018553 | 0.0027001 | 0.7009428 | 3.432352 | 0 | 183 | up |
| GSE9988_LPS_VS_VEHICLE_TREATED_MONOCYTE_DN | 0.0018975 | 0.0027001 | 0.7022270 | 3.429686 | 0 | 191 | up |
| GSE9988_ANTI_TREM1_AND_LPS_VS_VEHICLE_TREATED_MONOCYTES_DN | 0.0019011 | 0.0027001 | 0.6977299 | 3.403930 | 0 | 189 | up |
| GSE38681_WT_VS_LYL1_KO_LYMPHOID_PRIMED_MULTIPOTENT_PROGENITOR_UP | 0.0019120 | 0.0027001 | 0.6856263 | 3.336476 | 0 | 179 | up |
| GSE42724_NAIVE_VS_B1_BCELL_DN | 0.0019231 | 0.0027001 | 0.6795766 | 3.297390 | 0 | 178 | up |
| GSE42021_CD24LO_TREG_VS_CD24LO_TCONV_THYMUS_DN | 0.0019048 | 0.0027001 | 0.6754033 | 3.295617 | 0 | 185 | up |
| GSE22589_HEALTHY_VS_SIV_INFECTED_DC_UP | 0.0019120 | 0.0027001 | 0.6695782 | 3.258381 | 0 | 179 | up |
| GSE9988_ANTI_TREM1_AND_LPS_VS_CTRL_TREATED_MONOCYTES_DN | 0.0018975 | 0.0027001 | 0.6667556 | 3.256443 | 0 | 191 | up |
| GSE9988_LPS_VS_CTRL_TREATED_MONOCYTE_DN | 0.0019120 | 0.0027001 | 0.6664943 | 3.251515 | 0 | 193 | up |
| GSE3337_CTRL_VS_16H_IFNG_IN_CD8POS_DC_DN | 0.0019194 | 0.0027001 | 0.6661061 | 3.243824 | 0 | 180 | up |
| GSE6269_FLU_VS_E_COLI_INF_PBMC_UP | 0.0019417 | 0.0027001 | 0.6823938 | 3.229015 | 0 | 153 | up |
| GSE43863_NAIVE_VS_LY6C_LOW_CXCR5NEG_CD4_EFF_TCELL_D6_LCMV_DN | 0.0019380 | 0.0027001 | 0.6680005 | 3.226660 | 0 | 173 | up |
| GSE42021_CD24HI_TREG_VS_CD24HI_TCONV_THYMUS_UP | 0.0018553 | 0.0027001 | 0.6583079 | 3.223580 | 0 | 183 | up |
| GSE37532_VISCERAL_ADIPOSE_TISSUE_VS_LN_DERIVED_PPARG_KO_TREG_CD4_TCELL_DN | 0.0019048 | 0.0027001 | 0.6917367 | 3.213316 | 0 | 128 | up |
| GSE9988_ANTI_TREM1_VS_ANTI_TREM1_AND_LPS_MONOCYTE_UP | 0.0019194 | 0.0027001 | 0.6586656 | 3.212405 | 0 | 194 | up |
| GSE23568_CTRL_VS_ID3_TRANSDUCED_CD8_TCELL_UP | 0.0018939 | 0.0027001 | 0.6586150 | 3.212229 | 0 | 187 | up |
| GSE22886_TCELL_VS_BCELL_NAIVE_UP | 0.0019011 | 0.0027001 | 0.6582875 | 3.211507 | 0 | 189 | up |
| GSE360_L_DONOVANI_VS_B_MALAYI_HIGH_DOSE_MAC_DN | 0.0018622 | 0.0027001 | 0.6515805 | 3.193919 | 0 | 184 | up |
| GSE21546_UNSTIM_VS_ANTI_CD3_STIM_DP_THYMOCYTES_DN | 0.0018553 | 0.0027001 | 0.6495656 | 3.180770 | 0 | 183 | up |
| GSE21670_UNTREATED_VS_IL6_TREATED_CD4_TCELL_UP | 0.0019120 | 0.0027001 | 0.6513792 | 3.169819 | 0 | 179 | up |
| GSE360_L_DONOVANI_VS_T_GONDII_MAC_DN | 0.0019048 | 0.0027001 | 0.6490942 | 3.164098 | 0 | 188 | up |
| GSE9988_LOW_LPS_VS_VEHICLE_TREATED_MONOCYTE_DN | 0.0019048 | 0.0027001 | 0.6487939 | 3.163330 | 0 | 190 | up |
| GSE24634_TREG_VS_TCONV_POST_DAY3_IL4_CONVERSION_UP | 0.0018832 | 0.0027001 | 0.6459728 | 3.160821 | 0 | 182 | up |
| GSE9988_ANTI_TREM1_VS_VEHICLE_TREATED_MONOCYTES_DN | 0.0019048 | 0.0027001 | 0.6477552 | 3.158266 | 0 | 190 | up |
fgp <- fgsea_plot(fgsea_res$res_msg, pathways_title='All signatures', condition_name='BAP1 low vs high')
kable(fgp)| pathway | pval | padj | ES | NES | nMoreExtreme | size | state |
|---|---|---|---|---|---|---|---|
| chr19p13 | 0.0018416 | 0.0064626 | 0.7507847 | 4.070163 | 0 | 544 | up |
| GSE9006_TYPE_1_VS_TYPE_2_DIABETES_PBMC_AT_DX_UP | 0.0019493 | 0.0064626 | 0.8136341 | 3.906648 | 0 | 187 | up |
| GINESTIER_BREAST_CANCER_ZNF217_AMPLIFIED_DN | 0.0019011 | 0.0064626 | 0.7426209 | 3.781248 | 0 | 308 | up |
| GSE9006_HEALTHY_VS_TYPE_2_DIABETES_PBMC_AT_DX_UP | 0.0019417 | 0.0064626 | 0.7489666 | 3.585050 | 0 | 181 | up |
| chr9q34 | 0.0019646 | 0.0064626 | 0.7295889 | 3.541764 | 0 | 210 | up |
| GSE45837_WT_VS_GFI1_KO_PDC_DN | 0.0019455 | 0.0064626 | 0.7381046 | 3.536428 | 0 | 180 | up |
| GSE16385_MONOCYTE_VS_12H_IL4_TREATED_MACROPHAGE_DN | 0.0019380 | 0.0064626 | 0.7370112 | 3.535072 | 0 | 183 | up |
| GSE369_PRE_VS_POST_IL6_INJECTION_SOCS3_KO_LIVER_DN | 0.0019493 | 0.0064626 | 0.7339672 | 3.524129 | 0 | 187 | up |
| MORF_UBE2I | 0.0019194 | 0.0064626 | 0.7133588 | 3.492641 | 0 | 219 | up |
| MORF_PHB | 0.0020080 | 0.0064626 | 0.7680946 | 3.447925 | 0 | 113 | up |
| GSE9601_UNTREATED_VS_PI3K_INHIBITOR_TREATED_HCMV_INF_MONOCYTE_UP | 0.0019646 | 0.0064626 | 0.7267557 | 3.435344 | 0 | 162 | up |
| SPIELMAN_LYMPHOBLAST_EUROPEAN_VS_ASIAN_UP | 0.0018939 | 0.0064626 | 0.6407552 | 3.421352 | 0 | 444 | up |
| MORF_NME2 | 0.0019380 | 0.0064626 | 0.7289640 | 3.405198 | 0 | 141 | up |
| LU_EZH2_TARGETS_UP | 0.0019841 | 0.0064626 | 0.6838918 | 3.397405 | 0 | 257 | up |
| RICKMAN_METASTASIS_DN | 0.0019493 | 0.0064626 | 0.6842922 | 3.394247 | 0 | 246 | up |
| GSE9988_LPS_VS_VEHICLE_TREATED_MONOCYTE_DN | 0.0019646 | 0.0064626 | 0.7022270 | 3.375732 | 0 | 191 | up |
| GO_VIRAL_GENE_EXPRESSION | 0.0019531 | 0.0064626 | 0.7022003 | 3.368209 | 0 | 185 | up |
| GSE36527_CD69_NEG_VS_POS_TREG_CD62L_LOS_KLRG1_NEG_DN | 0.0019380 | 0.0064626 | 0.7009428 | 3.362070 | 0 | 183 | up |
| MORF_NPM1 | 0.0019763 | 0.0064626 | 0.7185991 | 3.354154 | 0 | 149 | up |
| MARTENS_TRETINOIN_RESPONSE_DN | 0.0018149 | 0.0064626 | 0.6052181 | 3.353928 | 0 | 722 | up |
| MORF_ANP32B | 0.0019380 | 0.0064626 | 0.6985141 | 3.350421 | 0 | 183 | up |
| GSE9988_ANTI_TREM1_AND_LPS_VS_VEHICLE_TREATED_MONOCYTES_DN | 0.0019724 | 0.0064626 | 0.6977299 | 3.348345 | 0 | 189 | up |
| MARTENS_BOUND_BY_PML_RARA_FUSION | 0.0019342 | 0.0064626 | 0.6332474 | 3.346672 | 0 | 418 | up |
| MORF_CSNK2B | 0.0019417 | 0.0064626 | 0.6701245 | 3.342085 | 0 | 258 | up |
| MORF_ACTG1 | 0.0020325 | 0.0064626 | 0.7308713 | 3.335667 | 0 | 127 | up |
| MORF_AATF | 0.0019646 | 0.0064626 | 0.6924533 | 3.328748 | 0 | 191 | up |
| REACTOME_EUKARYOTIC_TRANSLATION_INITIATION | 0.0020284 | 0.0064626 | 0.7426040 | 3.327944 | 0 | 112 | up |
| MORF_AP2M1 | 0.0019194 | 0.0064626 | 0.6851841 | 3.321971 | 0 | 203 | up |
| WELCSH_BRCA1_TARGETS_DN | 0.0020325 | 0.0064626 | 0.7266808 | 3.316542 | 0 | 127 | up |
| MORF_FBL | 0.0020325 | 0.0064626 | 0.7240208 | 3.313485 | 0 | 129 | up |